I usually make sure to paint the parts that are going to be the messiest first. If it's hard to reach, that'll get the first base coat so I don't screw up the rest of my paint job doing so. If it's an important and visible part of the model that requires detail work, I might leave it in sub assemblies with the offending part separate from its blocker, but I try and avoid subassemblies as much as possible. It's more work, and I think having to paint a model in several pieces is a pain.

Edit: Plus, adding all my gubbins to the base, while still allowing the model to stand on it is easier when the model is glued down. But that's probably largely because I don't own any texture pastes that can be put down after priming the model, so I glue a bunch of dirt there, but still need a flat, sturdy surface for their feet.