Water in Transmission...

Yes indeed. You have a transmission line connected right to the bung where the pet **** for the radiator drain is supposed to go. The transmission line bungs are always on either side of the tank and never that close together.

That said, There's no way in this universe I'd trust that transmission now. No way no how. It come out and back down to get cleaned up. Think about what had to happen. You said water and transmission fluid came out of the dipstick tube. That transmission had to be SLAM FULL of water. It's done as it is. End of story.