Sounds like you need to move to higher ground.
I'll take this with the wink. You do not always get a choice is Tas about where camp. But now I think about it some of the highest campsites were the wetest, Mount Massif (though this did drain very well) PB, The Labrynth for example.
So your tent floor is clean but your ground sheet or footprint is dirty? What is the difference?
I'm not sure of your point about puncture resistance. I'm not sure that a thicker floor is any less puncture resistance than 2 layers of thin fabric. I'd have to do a real test of this to be convinced either way. Over the years my macpac floors have demonstrated very good puncture resistance and worn very well. I have shared tents with other folks who have floors that leaked simply because of wear over the fabric.
I think thinner floors are solely so the marketing can say "our tent is lighter than your tent". And I would hazard a guess that most of the lighter floor fabrics are cheaper than a really good floor fabric. So marketing again can say "our tent is cheaper than your tent". I do not think it has anything what so ever to do with the functionality of the tent except that it is lighter. But there is no point in being lighter if it ultimately does not work.