About the problem with the thermal vias:

Why filling a via with epoxi when you have thermal problems?
Only a few percent of the the heat will pass through the epoxi.
Do some simply thermal calculation and you will se. The thermal
conductivity of copper is about 100 times better than filled epoxi.
A via that is filled with tin-lead will have a lot better thermal
performance.
Filling a via with something will also stress the via during the
processes and during operation. That has also to be investigated.

The best and cheapest way to have good thermal vias is to have a large
area of copper in the thermal vias. That could be made by large via
diameters and/or thick copper thickness.

Don`t forget to have a good thermal contact between component and the
thermal vias.

Christer Marklund