Unable to prevent pad file issues on ASUS Z77 Maximus V Formula

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System

Motherboard: ASUS Z77 Maximus V Formula
BIOS Version: 1902
GPU: AMD Radeon RX 6600 XT
[N/A] CSM is turned off. Make sure to confirm this in the BIOS and not with GPU-Z or similar since it can be inaccurate
[N/A] 4G decoding is enabled. Make sure to confirm this in the BIOS and not with GPU-Z or similar since it can be inaccurate
[Yes] UEFIPatch is applied (see Using UEFIPatch for more information). On some motherboards DSDT Patching is also needed
[Yes] I have read Common issues (and fixes)

Description
UEFI Patch applies patches to BIOS after injecting ReBAR module. An extra pad file is created - presumably because runtime, pcibus, and pcihostbridge modules change sizes.

Attempting to extract the modified modules and reinsert them in an unpatched image reproduces the pad file issue. This occurs with both MMTool and UEFITool.

I have seen some suggestions of manually patching the modules, but I can't figure out how to do this. When I attempt to do this, I can only find the bytes that need to be patched if I decompress the modules. If I decompress the modules, I can't seem to recompress them and reinsert them.

What can I do to correct this pad file issue?