As long as the derailleur can handle small/small with each cassette, it should all work.

The long cage *may* be slower shifting, doubt you'd notice.

I have never tried a 9s RD on a 10s setup, but am led to believe it will work just fine. I have one in the parts drawer, just in case.

Given your scenario, I would use the LC Chorus, and never think about it again. As long as the chain doesn't rub on the bottom of the cage in the 12-25, it will work without adjustment on the 13-29.