In its current state, FF4kster is not a fan of nonstandard rom sizes. In fact, file size is currently how it checks whether the rom has a header.
One trick you can use for any size expanded ROMs is to divide the filesize by 4Mb/512KB. If there's a remainder, the ROM has a header (or wasn't expanded properly). 4Mb is a safe value to use since the next biggest expanded size is 12Mb.
Though really, if you don't want to add support, it's not that big of a deal. Anyone capable of expanding the ROM and making use of that space is capable of extracting data from one ROM and inserting it to another. The only thing expanded support would be nice for is if you decide to support J2e's FF4 translation down the road.
