Does the PBR pipeline support this lightmapping technique?
Technically "yes." accurately, no.
Baking for PBR is more involved as you need to capture the directional component for specular response apart from just the diffuse response, the application of the lightmap then needs to go through its paces so the two are balanced correctly.
If Filmic Blender also applies to Blender's baking and not just final renders then it's probably doable from cycles with some math misery so the blender and R/T render sides are happy, as long as the desired method is simple (HL2-RadNorm or Amb+Dir).
I'm also curious about the object itself: if i need to use the same object in another level, can i safely bake another map, put it in UV2, and call it a day?
Yes. Though batching isn't set up with lightmapping in mind, and it's not really possible without a set in stone "this is how lightmaps shall be."