I created this conversion guide 1-2 years ago that will clarify many of your questions:
http://www.mediafire.com/view/umm5vkq0jjt91v6/converting_CHD_CF_Guide_2.pdf
Basically the 3rd track of a GDROM usually contains a big BIN file, which must be decrypted. This file is identicall to the content of the ROMs of a Naomi cartridge, only that the ROMS have been splitted in several chips and encrypted with a different method. There are 4 types of cartridges protection called M1, M2, M3 and M4. IF you concatenate the files in the proper order and decrypt the cartridge, you'll end up with a proper BIG bin file that can be netloaded or CF-loaded with a ZEROKEY PIC.
If you check mame's driver here:
https://github.com/mamedev/mame/blob/master/src/mame/drivers/naomi.c
for example line 5401 for TOTD, you'll see which roms must be loaded in which order. You'll see also in line 5430 that it uses m2 encryption.
You can just take mame source code, modify the code of the naomi driver, so that right after the game is loaded you save a decrypted version in a bin file.
All this information is publicly available thanks to MAMEDEV guys, so......consider giving something back like i.e. donating.