You mean you've installed Clover on all volumes ? Why would you do that ?
I think at least 2 instances is realistic, in case of a broken local installed instance of clover which doesn't boot, a second installed instance of clover on a external USB or from the Clover ISO CD version must be able to do the re-install/fix of the internal volume. Of course I see no reason of having multiple instances of clover installed and active alltime, but at least in a recovery scenario it must work without conflict. Still no one? I have this problem on multiple systems.
Can't talk about Chimera here, but i have chameleon boot file + Extra folder on the same EFI partition like Clover, with other kexts aswell, but they never get loaded from Clover...
I think it does need the option "WithKexts" to conflict with /Extra/Extensions. ###### installes some ElliotRTC..kext installed in /Extra/Extensions while booting clover it shows :-D up in the console with yellow letters cannot load that kext. This patch was not in the /EFI/Kexts/ directory nor some where else in that volume.
I use USB stick with MBR scheme, formated with HFS+ partition for external clover and internal disks are GUID scheme with clover as MBR install on the active HFS+ volume, the real EFI partition isn't used. I'm booting all the systems in BIOS mode.
Next week I will be able to test real MacPro1.1/2.1 again with clover(they gave black screen, I think because real refit was installed). I can also make some VIDEO bios dumps for Nvidia gtx 640 2GB versions, if there still needed for the high resolution bootscreen patch.