It generally covers original material themed on Star Trek too. Copyright doesn't necessarily mean an exact copy, otherwise you'd see plenty of things that are just slightly off to skirt copyright laws. Essentially, you're violating fair use if you profit off of the creation of anything pertaining to the Star Trek franchise that's not licensed.
Generally most of this sort of stuff they won't find out about, mind you, especially since a transaction like purchasing a custom theme is generally done privately. As long as you're not trying to sell a Star Trek-related theme openly and publicly, it's not a huge deal, especially considering a lot of themes wouldn't even be possible without paid stylists.
I bet everyone violates copyright law at least twice a day without realizing it.