PCI slot configuration table is different between 2A4X5H21 (F000:4A90) and 2A4X5O0HC (F000:7A9F). I have copied the table to 2A4X5H21 - fortunatelly it has less slots, if it had more, then I would need to relocate it.
Here is another patched version. Unfortunatelly 86Box does not assign the interrupts even with your original BIOS so I cannot properly test it.
I am using Modbin4 to unpack and repack, Hiew 6.11 for interactive editing, AwdHack as a Modbin wrapper to run Hiew just before repacking (for this purpose I use Hiew 2.51 as it requires much less low memory), ndisasm for listings, less and grep for paging and filtering.
The workflow for a pair of compressed 128KB BIOS is:
1) open a bios with Modbin4, it unpacks the image and creates a temporary file called "original.tmp" that I would use later;
2) run "ndisasm -b 16 -o 0xe0000 original.tmp" and keep the listing;
3) repeat steps 1-2 for another BIOS, compare the listings by finding rare instructions - to find PCI slot configuration table, I used this regular expression: "mov e..,0x40......$" - the following mov si,imm32 points to the table;
4) open both files in Hiew 6.11, go to code mode (enter, enter), set offset (ctrl-f5, e0000), go (f5) to the code that was just found, set a bookmark (+), walk around (pgup/pgdn/0-9) to check the surrounding code and then return back (-) if needed;
5) make a plan of the changes - make instruction patches in a temporary copy using Hiew to get it assembled if needed to get the hex codes;
6) run AwdHack - it would run Modbin4, then just use the top option to update the file - AwdHack would intercept that and drop you into Hiew 2.51;
7) apply the planned changes in hex (remember there is no offset option, so E000:0 is just 0 but F000:0 is 10000), save and exit Hiew;
😎 AwdHack would pass the changed original.tmp back to Modbin4, which would repack it.
To verify the changes, I use vbindiff (for visual inspection) and 86Box (to actually run the modded image).
If I need some more complex rework, I would use Ghidra and spend a few hours mapping the structures and subroutines.