rjdunlap's planets seem intended to replace the vanilla planets in various combinations, I was excited to pick a few and have a brand new playthrough, but, having them be moons of the vanilla planets that I don't want to use seems frustrating. It would be nice if we had individual settings to delete each vanilla planet.
The simpler implementation would probably try to "promote" 1 moon to replace each deleted vanilla planet, preferring (or only considering) rjdunlap's planets? And just throw an error if there's no moon to promote, so that we don't have to consider actually removing nodes?
However I don't really know what ramifications this has on tech/progression, so, maybe it's still difficult.

Even with the current setup, setting your starting planet to one of these moons gives Muluna a broken orbit with no connection, so a Froodara or etc start seems impossible.

Hello, it's a bit different scope of work, that mostly not related to this mod. About 'Any Planet Start' mod and rjdunlaps planets (and Muluna, as a moon) it's an issue for their developers.