That is why triple insulated wire exists, it is a standard thing in transformer winding.
Also, those mylar tapes used inter winding are tough and as long as you design the windings to ensure sufficient creapage around the edge of the tape, a few layers is just fine and I would have no concerns.
The issue with PCBs is surface contamination and that FR4 fairly readily carbonises leaving conductive tracking, been there, seen it, not much of an issue in a transformer, which has at least two thicknesses of insulation to fail even if you took no precautions what so ever (And as I say, triple insulated wire exists for a reason).
Regards, Dan.