Yes, I know that it's not possible to combine bin/cue and sbi files to a pbp file. The way it should work though is, that the emulator should find a sbi file in the folder, checks the file name and matches it to the corresponding pbp file. This is already working with single-disc pbp's and single sbi's, but it seems like there's no way with FPse64 to link multiple sbi's to different discs of a single multi-disc pbp.
In Retroarch this already works by using this syntax
[filename]_[disc_number].sbi instead of [filename].sbi if(PBP_DiscCount > 1)
But it seems this isn't supported right now in FPse64.