Good news and inconvenient news:
The functionality issue with Star Trek Online's launcher/patcher has been fixed in Crossover Games 10.1. The launcher/patcher should run smoothly, now, provided that your STO bottle does not have the HTML 7 engine workaround applied.
If you applied the HTML 7 engine to your STO bottle in order to work around this problem in Crossover Games 10.0, your patcher's behavior will not change. In CX Games 10 the patcher/launcher would work after applying HTML 7, albeit with tremendous flickering and rendering problems. HTML 7 overrides the fixes in our code that solved the patcher problem.
So - if you did apply the HTML 7 engine workaround to STO, you will need to re-install STO into a new bottle with Crossover Games 10.1 to get a smoothly functioning launcher/patcher. If not, STO will continue to function, but the flickering and rendering issues on the launcher won't go away.
Ken Thomases