I'm currently setting up my own server, and am using the legendary clause for all gym leaders. However, I tested it and got myself a team of legendaries. It actually allows me to select Mewtwo for my team when I challenge them, but not others. It might be worth mentioning that before I got any other legendaries, I just gave myself a team of mewtwos for the sake of testing, and they all worked. Then, I added a raquaza. Didn't work. Then I tried Mew, Latios, and Groudon, all didn't work. A dev recommended I try Ho-Oh to see if that changed anything. Didn't work. Same goes for the gen-1 legendary birds. It seems very likely only mewtwo works. I'm on the most recent update. If you'd like to see what it looks like, here's a printscreen. http://prntscr.com/fkn9if

I tested this with every legendary in the game, including alternate forms, turns out Regigigas isn't affected by the clause, too.