Take a CUE/ISO/WAV TGCD disk image and burn it to disk, then re-rip it. Do this 10 times, and the crc/hash/ect of the file will be identical to the one you started with (assuming you're using good ripping/burning software).
Take a CUE/BIN image of a TGCD game, burn and rerip it ONCE, and you'll get different file sizes. By the second time you did this, you'd be lucky to get an emulator to load the image (or the actual hardware to load the disk) anymore.
File sizes are VERY important with a TGCD backup.
At least for the type of data disk TGCD games are you CAN NOT properly back them up ANY way except CUE/ISO/WAV.
I've followed the TG16/TGCD emulation/backup/preservation for about 20 years now, and this was a MAJOR issue with backups until NightWolve made TurboRip, which allowed for perfect rips almost every time.
Oh, and CUE file problems for TGCD games should be handled by TOCfixer (http://www.ysutopia.net/index.php?ind=downloads&op=entry_view&iden=4), not Sega CUE Maker. TOCfixer can also help you properly covert those crappy CUE/ISO/MP3 backups you find to proper CUE/ISO/WAV backups.