It's the jumbling of issues from which the transphobia comes from, Seriati.
The original "complaint" was that the woman couldn't get her money back because she saw a person with a penis in the women's locker room. This caused protests against the spa. Is that not correct?
No. That's not correct.
I repeat, that is not correct.
That's how it was reported by certain people, which generated a controversy.
AFAIK, there was no mention of an erect penis in the original complaint. And it is a well-known trans-friendly spa, so how could she be surprised to see a penis in the women's locker room? 
Why don't you read that again. Why would someone at a trans-friendly spa be surprised to see a penis? They wouldn't be.
They would be surprised to see a man with an erection staring at them while they're changing or partially nude. Heck they might report something like that to management....
I certainly don't remember Crunch mentioning an erect penis.
And how much research exactly did YOU do on the point before you ASSUMED it was a transphobic attack? It wasn't an obscure story, it was widely reported, but a large large number of the reports were silent on significant details - that's a big tip off that there's more there than the writer wants you to see.
Furthermore, even if the penis was erect, why is this the spa fault? The person who displayed his genital thusly is the one responsible for it, not the spa.
Because it was reported to the spa and they decided to treat it as trasphobia rather than deal with a sexual predation. That's exactly how the Catholic Church and the Boy Scouts become "responsible" for the actions of predators in their ranks.
Face it, it's human nature to explain away a situation where two people are telling contradictory stories (a classic he said, she said, for example) in the way that involves the least action on their own part. They don't know what happened so they extend the benefit of the doubt to the person that they believe is more aligned with themselves. It's not hard to see why a trans-friendly spa would choose to believe the person that they believe is trans rather than the person they believe is the bigot.
If the spa was aware that the individual was registered sex offender with multiple sex and non-sex related convictions would they have handled it the same way? Very doubtful.
If the spa allows biological males in the women's locker room so long as they keep their junk in the normal condition, and everyone knows this can or will happen, how are they to enforce the status of that junk?
They can throw the person out afterwards, or hand them over to the police, but that's about it.
They should in fact remove the individual if the situation appears deliberate. No one should be held accountable merely for getting an erection, but combine that with lewd looks and it takes on a different connotation.
Here they could also have refunded the money to the person that was assaulted (that's just good business though).
So why were there protests against the spa?
Because like you, people on the other side assumed the situation and were offended.
Why blame them for allowing trans people to use the women's locker room?
Because that's the "but for" proximate cause of the issue.
And as I asked before, if this happened at a nudist colony, would there be right-wing protests calling for the closing of all nudist colonies because they allow exhibitionists to display themselves in front of girls?
Nudist colonies face legal problems all the time, and not just from the right. Whether you get it or not people on the left are just as nasty about issues in their back yard. They want nudist rights for people in other communities, or even other neighborhoods. I've lived around elite leftists for decades and they are overwhelming virtue signally persons that are also racists, sexists and homophobes. Everyone of them puts a sign in their yard supporting gay rights until their kid starts dating someone of the same sex, they pass any number of ordinances and restrictions to prevent any poor black or brown kids from being able to intermingle with their own kids and if those fail they pull their kids out of school and send them to private schools or private club activities and then they put a BLM poster in their yard to show their solidarity.
Do you somehow believe that that has never happened, that these perverts, who you believe are perfectly willing to dress and act like women all of the time, would pass up this easier opportunity?
First of all, it's only your delusion that requires they dress as women all the time. Do you think the spa conducted a background interview of every person to confirm that their decision was a full time choice? Again, you're mixing up trans people with predators. Predators do what it takes, and yes they would dress full time if they had to in order to maintain access.
But more relevant, nudist colonies, Boy Scouts, even the Catholic Church are much harder targets specifically because they've been hit before and are on guard. Every adult that spends time with a Boy Scout troop (even a parent that goes on a camping trip) has to go through training to spot and report harrasment. Effectively the Boy Scouts view every adult as a mandatory reporter. Do you think any woke spa believes that's necessary?
For the moment, trans-friendly policies implemented by the ideological are hampered by attitudes like you're expressing that to take precautions is somehow offensive to trans people. But ask yourself why? Why on earth would trans-people want to protect predators? They don't. They don't want to be falsely accused of being predators for living their lives, but that's actually a different issue. Your overreaction is literally counterproductive. The goal should be to create a trans-friendly environment WITHOUT opening the door to the level of abuse we've seen in other organizations that didn't believe they had to be on guard. People on your team need to wake up and relax the ideology to accept that some people will abuse ANY situation and that implementing reasonable safeguards in advance will protect trans people and prevent backsliding counter reactions.
Or do you think that everyone still has exactly as much respect for the Catholic Church as they did before the scandals were revealed? You already know the answer, some people will ALWAYS hate that church and even it's innocent members. Is that really where you want to see transfriendly policies end up?
If so, why haven't we seen such violent protests for the past 90 years or so? 
Because the point is nonsense and nudists have going out of their way to keep their activities private.
The outrage is not because this was a spa where males were allowed to walk naked in front of females. It's because this was a spa where trans people were allowed to walk naked in front of females. That's the source of the outrage, for the protesters and for Crunch.
So would you see problem with a spa that advertised that women and children are nude and that men are permitted to watch them and masturbate?
Why are you reducing the issue to eliminate considering an uncomfortable problem? Whether or not the "other" side has bad or good motives - and you really don't know - your defense is still wrong. You're hurting trans people by refusing to accept that predators can be differentiated from them.
The guy's been charged. He'll have his day in court. He's being treated just as if he were a cis man walking into a women's locker room and showing his erect junk. It could happen at any bathroom anywhere at any time. So why is this somehow trans people's fault since it happened at a trans spa?
I can't even fathom the pretzels you're working through in your mind to frame that question. Maybe point out the "nudist" spa that allows men and female children to be in the same area and has no issue with the men having erections and staring? Can you even find one outside of Thailand?
By the way "cis" is a nonsense word crafted to sound negative. Maybe if you're going to hold to your ideals you should reconsider using it, unless you think other words that are negative that describe people's gender, race and sexuality are also okay to use?