When playing Mine while having a Watchtower in hand, can you put the upgraded treasure card on top of your deck instead of in your hand?
Yes, you can. The card you get from Mine is definitely gained, therefore you can react to it with Watchtower and put it on your deck (or trash it!) if you like.
There's not usually much reason to do so, but the cards don't actually conflict - you can use them both in this manner if you really want to.
From the Prosperity rules pg. 5:
If a gained card is going somewhere other than to your discard pile, such as a card gained with Mine (from Dominion), you can still use Watchtower to trash it or put it on your deck.
I think it's great that Dominion always includes blurbs in their rules for each card. They seem to have anticipated most rules questions.
Mine says you are gaining a card. Watchtower says you can reveal the Watchtower from your hand and either trash or put the gained card on your deck.
Found a game log reference on councilroom.com showing this exact situation:
bandito plays a Mine. ... trashing a Copper. ... gaining a Silver in hand. ... ... revealing a Watchtower and putting the Silver on the deck. (bandito draws: a Silver, 3 Coppers, and an Estate.)