ds roms are compiled as binaries to 32-byte alignment. their page size is 512 bytes. there are 2 types of ds card, actually: maskrom and one-time prom. maskrom has a much faster transfer rate(6MB/sec vs 1.5MB/sec) on access, while the prom is faster when it comes to many quick, successive card accesses. the prom can also go up to 4gbit in size, whereas the maskrom can only go up to 512mbit. dsi hybrid and limited games are prom-only, so bw1 and bw2 are all prom games. actually, all the pokemon games are probably prom.
anyway, what i was getting around to saying is that the reason it's expanded and filled with FFs is by nintendo's mandate. depending on the size of your chosen card, and regardless of rom type, the last part of the rom is made up of a few pieces. roms which are 128mb and above have a use-forbidden region at the end which gets bigger as you increase in rom size. this region is mandated to be filled with nothing but FFs as part of the build process. the rest of the end is made up of(if it's a dsi hybrid or limited rom) the arm7i bin, the arm9i bin, and overlays for the arm9i- none of which any current dumper has any chance of handling, so you end up with more FFs. the last piece is actual unused space, which is also mandated to be filled with FFs by nintendo.