When a CD is being booted, the firmware checks the CD for a "boot catalogue" in the CD's meta-data. This is a list of entries with (up to) one entry for each kind of computer; so that it's possible to create a single CD that works for 80x86 BIOS and 80x86 UEFI (and PowerPC and Sparc and ...).
For 80x86 there are 4 different types of entries:
UEFI. The rest of the entry tells the firmware the starting sector and size of a FAT file system image. UEFI figures out which file it wants from the FAT file system based on converting the architecture into a file name (e.g. for 80x86 it'll probably want the file \EFI\BOOT\BOOTX64.EFI).
"No emulation, 80x86 BIOS". The rest of the entry tells the firmware the starting sector and size of a boot loader. The boot loader can be any size you like (up to about 639 KiB); and the "device number" the BIOS tells you (in dl) will be for the CD drive itself, so you can load more stuff from the same disk using it.
"Hard disk emulation, 80x86 BIOS". The rest of the entry tells the firmware the starting sector and size of a disk image. The disk image should have an MBR with a BPB and partition/s, with an active partition pointing to where the operating system's boot loader is at the start of its partition. In this case the BIOS will create a fake "device 0x80" (from info in the BPB in the MBR) and mess up the device numbers for any real hard drives (e.g. the first hard drive which would've been "device 0x80" will become "device 0x81" instead, etc). Note that this is inefficient because sectors on a CD are 2048 bytes but the BIOS will emulate 512 byte sectors, so every time you try to read a 512 byte sector the BIOS will actually read 2048 bytes and throw the "wrong" 75% of the data away. It's also very annoying (trying to squeeze anything good in 512 bytes is impossible). It's mostly only used for obsolete junk (e.g. MS-DOS).
"Floppy disk emulation, 80x86 BIOS". The rest of the entry tells the firmware the starting sector and size of a disk image. The disk image should have a boot loader in the first sector with a BPB. In this case the BIOS will create a fake "device 0x00" (from info in the BPB in the MBR) and mess up the device numbers for any real floppy drives. Just like hard disk emulation, this is inefficient, even more "very annoying" (because it also limits the OS to the size of a floppy which is nowhere near enough space), and only intended for obsolete junk.
The best way to deal with CDs is to write 2 new boot loaders (one for "no emulation, 80x86 BIOS" and another for UEFI); then use any tool you like to create the appropriate structures on the CD (e.g. genisoimage with the -no-emul-boot option for your "no emulation, 80x86 BIOS" boot loader plus some other option for UEFI that doesn't seem to exist!?).
Note that it's easy to write your own utility that is "more clever". You'd want to create a FAT file system (for UEFI) and an ISO9660 file system (for the rest of the operating system's file - help/docs, drivers, etc), but most tools won't create the FAT file system for you, and it's possible for files in both file systems (FAT and ISO9660) to use the same sectors (so that the same files appear in both file systems without costing twice as much disk space). Something like this would probably only take you 1 week to write yourself (and you'll learn a lot about CDs and ISO9660 that you're going to have to learn eventually anyway). The relevant documentation (for booting from CD, ISO9660 file systems, FAT file systems, and UEFI) are all easily obtained online.
Also, what is El-Torito?
El-Torito is another name for the "Bootable CD-ROM Specification" that describes the structures needed on a CD to make it bootable.
