@mmh3 : Before I start checking all your modded BIOSes (you can expect my result tomorrow), here are my answers to your other questions:
The user should compare the structure of the original and the modded BIOS regarding the presence and location of Pad-files. If the modded BIOS contains at a certain location a natively not present Pad-file or a natively present Pad-file is missing, I don’t recommend to flash it.
Nobody can evaluate, whether a flashed modded BIOS with an added or removed Pad-file would work or cause a bricked mainboard.
I don’t offer (pre-)compressed FFS files, but the MMTool offers for the insertion of FFS files the options "As is" and "Compressed". If there is enough space within the "DXE Driver Volume", it doesn’t matter which option you choose, but sometimes it is necessary to choose the "Insert compressed" option to avoid the message "Not enough space".
By the way: All DXE Drivers will be compressed after the insertion, because the complete "DXE Driver Volume" is compressed (to be able to compensate the addition of a new module without changing the Volume’s size). The compression rate and the ability to add a natively not present DXE Driver depends on the uncompressed size of all DXE Drivers, which are within that Volume.
You should better ask the developers of the tools.
Only very few BIOSes have your reported problems. In such case it is time consuming even for a BIOS modding expert to find the perfect solution.