Yes, I'm well aware of the palette issues. Someone was courteous enough to send me screenshots of the relevant screens from an actual Indy with an 8-bit board running IRIX 5.3.
Currently I'm not quite sure why the palette is mangled, though I do know that I don't emulate the optional endianness swaps on Display Control Bus transfers. There's a chance that those palette entries are uploaded with that bit set, in which case the result would be more or less exactly as pictured. I'll be taking a look at it this evening.
