Some OS recovery disks have the setup files compressed in propietary formats like "win98.dat" that can only be decompressed with the "custom" install program you refer to.
One possible way to get to the OS installation files is to interrupt the install right where the "custom" setup ends and before the normal install is called. It depends on how the "custom" setup has been made however, some I have used have a routine to delete the files if the install is interrupted.
Also, as someone has already pointed out, the setup files in recovery CDs most of the time (if not always) have files suited for a particular hardware/brand and may not have all the drivers included in a "standard" OS installation CD. That's the case with the Windows 2000 Pro recovery CD we use at my work, it only works with a particular MB/BIOS/CPU combination, we have tried to use it on other systems (different brand, MB, and so on) and upon booting the "custom" setup inmediately replies "This Recovery CD can only be used on Ultra-PC systems!. Exiting setup"
The W2k files are not accesible from the CD since they are compressed into "win2ksp4.dat" (214Mb) and no decompression software we have tried recognizes the compression format of that file. It only gets decompressed by the "custom" setup routines that fires up upon booting.

And, as I mentioned, it only seems to have drivers for that particular system. Everything we added later, we have to download the drivers from the Internet.