Yes and No.
You can use different BIOS pointing to a different location but AFAIK you cannot use two X3 BIOS with different settings, as they would overwrite each others settings.
From the live config, set your X3 BIOS to boot from let's say "E:/XBM/default.xbe" (not a typo, you cannot set it as E:/XBMC... it will complain the path is too long)
Then use any BIOS you like on other banks, you just need to edit an older X2 BIOS with XBTool or edit the config file of the latest X2 or iND-BiOS to fit whatever you like.
And don't use a single 1MB BIOS on top of the X3 one, use four 256KB BIOS, one 512KB and two 256KB or two 512KB.
