I’ve been doing the second, and yes it’s very messy…
However, this addon looks to be a decent solution: [Addon] Bake Wrangler - Node based baking tool set (Ver: b0.7 *imageset*)
There’s a few others that combine materials in baking as well, but that one has the smoothest, least fiddly workflow I’ve found-- it’s just not quite finished/polished.