Kokoro is canon, even if she's not in that ending. It's just that she will show up later. ^^;
Technically, depending on how I'm feeling, all three "good" endings are canon and may be extended in the future, even if not in a CYOA format.
The "join the team" most closely follows the overall story arc from the plotting and ideas this was based on (a story that never got written), but I have to admit a partiality to
stories where the character shifts from normal guy form to
superhero girl form and back at will -- though unfortunately, both of those stories/worlds are still in development and not continued at this time (and, technically, that's a spoiler for the first link... ^^;;; )
By the way, in case it was missed, it is written under a Creative Commons license allowing others to make their own derivatives of it (ie, continue off one of the endings, make a sequel, redo it, or even use the code to do their own CYOA) provided that it's not for commercial purposes, due credit is given, and any derivative/follow-on work follows the same license.
It's not the greatest example of coding in the world, though, so.... *shrugs*