Superpet, SP9000 & MicroMainFrame 9000 are all the same machine.
It's done in purpose. There are also a bunch of similarly "duplicated" entries in c64.c. The idea is to have an entry for each different model sold (see also many Sharp Pocket Computers or Sega SC3000/SC3000h or Dina's different Coleco clones), possibly with different artworks (e.g. if we start to implement clickable keyboard we will need good scan of the different PET2001 'chicklet' and full stroke keyboards).
The Pet 40xx & 80xx are pretty much the same as CBM 40xx & 80xx as well.
Only the old models. The new ones have a different ROM with support for 60Hz / 50Hz CRTC. And models with normal keyboard vs business keyboard have different BIOSes as well (to support larger chargen in the latter ones, and numbers only on the keypad in the former ones)
The commodore structure tree's although better than before are still generally pretty screwy.
If you read the notes at the top of the driver you'll see that it reflects much better the informations from here
I don't claim it's perfect, but I can ensure I spent hours to sort the previous mess (no pun intended) and the contradictory info you can find around in the web. The final goal is to make MESS source a reliable document about the original hardware (that's why there is no more CBM 20xx series, which is unconfirmed and probably fake: PET european models became CBM 30xx) and I'd like to improve it, if possible: if you find inaccuracies please be a little more precise than "are still generally pretty screwy"
And the PC/AT (VGA, MF2 Keyboard) should be placed in the IBM PC/AT 5170 tree
pc.c work is wip and only half done (see http://mess.toseciso.org/people:wilbert_pol ). newly added sets 5150, 5160 & 5170 (with clones) are actively worked on. old sets like pc, atvga and all the amstrad models are still in the previous (bad) shape, untouched. Judge will sort them out later for sure, when he's satisfied by the emulation status.