Actually, it's mentioned in the readme file that Schala is not a playable character. The story is simply changed to one where she escaped the Ocean Palace disaster after the Lavos incident. Here is what is written in the readme file for the zip download (which can be found in the link in the first post above):
Please note that Schala is not a playable character; Chrono Trigger
limits the game to just seven party members. Some ambitious people
are working on an eighth character expansion mod, but I think
that's still a ways into the future. This is something I'd like to
tackle someday, but... not now.
Even so, it's still nice to have a reason to replay this great game. And even better still that Schala gets out safely from the Ocean Palace in this version. I've always wanted to see a version where she and Janus get to live peacefully together after all they've been through. Quite frankly, I've had enough of drama in games...