Does the automatic minus in a category (resulting from not having enough dice to assign) count as a die that can be rerolled?
Probably a GM call.
I'd say yes.
If so, should a threatened or endangered category that doesn't have an actual physical die assigned be treated as having two/three automatic "virtual" minus dice, or just a single one?
The wording on pg. 98 (Interim Stage) seems somewhat ambiguous, but suggests the latter. However, in such a case math would go weird.
If, indeed, you were going to call things that way, it would certainly be odd not to "fill up" a threatened category with (-)s.
Bliss Stage does require the GM to make decisions in these circumstances.