I would not say that using a compatible will surely not work with FMCB, but there is a chance it could not. MagicGate was never an open standard and so compatible cards would have been made using reverse-engineered logic. Since the full command set is not required for authentication (and hence saves), we do have compatible cards that only work well for storing saves.
FMCB is just another save folder on the memory card, so you may also save your games to it. One reason to use a different memory card for saves, is to protect the one containing FMCB (particularly if it is a genuine card) from wearing out the NAND. But in that case, you might want to plug the FMCB card into slot 2, as the browser can boot FMCB from either slot but not all games and software support both slots.