@Bahamut: Like "OctaBech" said. It'll make no sense, the way you proposed FMCB to work.
It will make fastboot unusable.
Turn it of, or map your auto-ELF to a button, to start it, even if a disc is in drive.
If you delete the CNF, it will used hardcoded strings, so removing CNF-Feature is not necessary (in my opinion).
An easier way to auto/fast-boot esr-disc, is...
Detect if there is a disc in drive and which kind of media it is. --> If it is a CDVD, try fastboot, and if it is a patched DVDV --> Start the ESR.ELF (external, or included) --> else do the rest of the boot-process.
(But I'm not sure, how to differ between DVD-Video and DVDV-Patched disc.)
PS2 V7/DMS3 V2 (FW:2.4b7); Seagate Baracuda 200GB
PS2 V7/CC1.0 (FW:34 hacked v2 BM:2.1.6); Maxtor DiamondMAX9 PLUS 160GB
PS2 SCPH-30004R; NoMod+NoLaser
3xSony MC 8MB
MAX/Datel 16MB with Boot-CD
Custom FMCB 1.8b+ Beta-Build, my AIO 0.5, Sony&xRhino-Linux