Proper Protocol for “Complimentary Roof Inspection”

Looks to me like it bubbled from the inside out. That would indicate that there was some contamination on the roof when they did the caulking, probably grease or dirt on the vent flange. Seeing that the same person probably did the entire roof at the same time, I don't think it's unreasonable to suspect the entire roof.

I will say one thing - if I were buying that rig I'd walk away based on the lack of roof maintenance in general.