Hmmmm..... Now you got me thinking! lol.
Only thing I can think of is possibly a bad drain plug seal? It's been a while since I drained mine, but I seem to remember seeing an o-ring or a washer crush seal. But I could be wrong.
Perhaps draining it, then sealing the plug threads with silicone, refilling and watching might be a good place to start. Seems you've covered the inspection pretty well.
Mine has a nasty habit of the case-to-tail housing seal being bad. That'll be fixed when my spare trans is repaired and installed sometime in the Spring.
'01 XLT disguised as a '03 Fx4 Level II
Big. Loud. Slow. Bright.