Is this a padding file issue? Or is it safe to flash? DXE_ffs & patches.txt applied

[0x6A7232]

MSI MS-7972 (aka MSI z170m Mortar) with a 7700k & RX 6700 XT

Have applied DXE_ffs at end of PCI section (3C1DE39F-D207-408A-AACC-731CFB7F1DD7) using UEFITool 0.28 and then run UEFIPatch with patches.txt on the resulting file. Compared using UEFITool NE 0.70A as seen in screenshots. These are the only 2 padding file differences I could see.
E7972IMS.AC0 is the stock firmware image, on the right side of the screen in both screenshots.

[NikolajSchlej]

The first padding is inserted to make sure the microcode file remains aligned (it has alignment bits in the file header). Ideally it should be left at the same offset, or the link to it from FIT needs to be updated manually.
The second padding is problematic and needs to be fixed manually (open the original image in hex editor, copy the whole "Startup AP data" block, and insert it into the modified file manually at the same offset).

[0x6A7232]

Nuts. Is there a guide (preferably with screenshots) on how to do either of those?

Wait, if I do the second one, it's basically taking the stock (good padding) firmware, and manually inserting the section from the modded firmware containing both modifications into the stock firmware at the right location to keep the proper padding intact, right? So that is all I would need to do?

[NikolajSchlej]

1. Normally you do not need to change anything, UEFITool 0.28 should have done it for you.

2. The other way around. You take a modified FW with PEI volume modification that removed the Startup AP data array, and insert that structure back where it was in the original unmodified file. The structure is small enough (16 bytes) and is close to the bottom of PEI volume, so there's usually nothing there to interrupt the insertion, just 0xFFs.

More info in the original EDK2 GenFv tool source:
https://github.com/tianocore/edk2/blob/stable/202011/BaseTools/Source/C/GenFv/GenFvInternalLib.c#L106
https://github.com/tianocore/edk2/blob/stable/202011/BaseTools/Source/C/GenFv/GenFvInternalLib.c#L1744