X2.4981 is newer, and has LBA48 support for large drives, as do iND-BIOS.5003, Evox M8+, and X2.5035. They all "take stock of a big drive" whenever they are loaded, not just when XBMC runs. XBMC simply uses the partitions presented to it by the BIOS, it doesn't change the way the disk is handled. So, which BIOS did you find that you believe exhibited this problem?
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and I haven't seen anything as compatible as SID's nkpatcher11 (haven't tested other versions).
That's an interesting piece of self-fulfilling logic - you are unlikely to see any other compatible versions if you haven't tested them! If you're going to make claims like this then you should test all three major NKPatcher based softmods (SID, Krayzie, Kingroach) with your problem ROM/Emulator combination. More importantly, compatible with what - you haven't defined how you assess that any of the BIOSes or BIOS patchers is compatible?
FYI, NKPatcher in Krayzie and Kingroach is essentially the same as NKPatcher in SID, but if there are any differences in the way they support applications it would be useful to document them here.
More generally, can you share details of the specific problem you are trying to solve? Which ROM in which emulator fails with which BIOS? Which BIOSes did you test before concluding that the old X2.4977 was the best? Which ones passed, and which ones failed?