Just did a little bit of research on this, and this is from an article I found:
A word of warning, users have reported that link play [on My Boy!] only works between identical ROMs. That means no trading between Fire Red and Leaf Green, unfortunately.
A bit of a shame, but for anyone playing on an unofficial source like an emulator, you kinda have to deal with small drawbacks like that. Would be cool to see if there was something in the future that would fix situations like this, though.