So.. it's just like acquiring something from an online shop.
They have to package it, ship it, and you have to unpack it to finally gain it.
When-would-gain happens during packaging (oh no this Justin Bieber CD isn't right, it should be a Beyoncé CD, so let's put that inside the package)
Moving the card is shipping (it can get shipped to your house or your business address; if you don't specify an alternate address it will just be your home address)
When-gain happens during unpacking (hey look I found a Justin Bieber CD, let's trash it!)
Now, let's apply this metaphor:
You're gaining a Watchtower with Transmog, it gets shipped to your hand.
You unpack it, by simple looking at it and go "hey, a Watchtower!"
Now you can apply Watchtower's effect, since well, it's in your hand, right?
Did Watchtower lose track of itself? Well, it's in your hand as it should be, so I don't think so
Resolve Watchtower as normal.
Now, if you do this:
Have Royal Seal in play (due to BM)
Use Transmog to gain a Smithy
Apply Royal Seal to put it on top of your deck
--> At this point, has a Watchtower in your hand lost track of Smithy?