For Cataline I would wait for the kexts to be stable, while it is in beta it can change a lot and the developers like RehabMan have a hard time to track all the changes, so I would wait or experiment on a test partition or drive, before modding the main system partition.
I have not tried Catalina yet, but I have a stable install of the system in a 250 GB mSata SSD, that I installed in the early High Sierra days and survived through Mojave upgrade. I have the EFI partition and windows installed in a Sata3 480 SSD.
I have done it one time with my envy 15j, but the system is not optimized for boot from mSATA. If you have other system installed in the main drive it can be hard and you can't set the main boot from the mSATA.
If you leave the EFI partition in the main SATA drive, it is okay to have the other...
I was having similar problem with USB, bluetooth and camera not working, like @gaiaweylyn.
Was scratching my head for the last three days thinking about what I did wrong.
But now it is working fine!
Good job with new project structure,
don't forget to move config.plist to efi folder:
cp config.plist /Volumes/EFI/EFI/Clover/config.plist
And remember to run this after rebooting without caches:
sudo touch /System/Library/Extensions && sudo kextcache -u /
I was having a similar problem, now I have...