The FIT specs are there to ensure interoperability.
So everything that's defined in these specs can be decoded by other software that has implemented these specs.
If you leave this path and add new messages, of course other pieces of software don't know about your addons. If these pieces of software are coded well, your added messages won't hurt them - but they won't be able to decode them. How could they if they don't know about your additional messages?
Cheers,
OMB