OK, I think I figured this one out. Behind the scenes, GalCiv2 combines the political parties in any of the xml files in the PolticalParties mod folder (evidentally it doesn't matter what the files is named; it uses all of them) with the ones in the core game files. If you have parties with the same ID or name (could be either; I didn't change internal name) in the mod, their bonuses will be combined with corresponding core party, creating a mess of modifiers. To fix this, I commented out all the party info on the non-mod PoliticalParties (and I made a note to myself so I wouldn't forget!).
The result was I was able to have my custom list of parties as the only ones in the game.

However, in my sample game I noticed all four of the AIs had the same political affiliation . . . so my edits are evidentally screwing something up.

Ah well.