"Pad.kR : TopVia2 under Pad not allowed (Note 3)" is a valid DRC error? Any way to fix it?

It is a reliability rule. When you do wire bonding some of the vias can be destroyed but you have many in the bondpad we deliver. If you want to have a bulletproof design you should extend TopeMetal2 outside the bondpad area and place vias there.

It'd be nice to have the pad macro in the PDK itself btw ...

It is on the list of the upcoming PyCells