In this case, some ways you can explore yourself to understand the problem:
- compare a workable with-thunar template with your minimal template : where are the thunar extensions? How does it work? Rule policies, …
- compare in qubes-core-agent-linux, the thunar files with the nautilus files : thunar vs nautilus
- search in the issues a thunar related problem
- search in the forum a thunar related problem (example]
And you can explain here the ways that you find.
Finally maybe it will end with a bug report…