Congrats and welcome!
You'll find a ton of information in these forums from those that have come before you, so whatever your potential issues may be (knock on wood, none), rest assured others have likely experienced them and the answer to the solution is to be found here.
Search is your friend, but it does take some getting used to. The sheer amount of volume of material to read will seem daunting, but in my 14 yrs of being a member I can say I've learned a little something from every thread I've read. In the end, your TDI will thank you and your dieseling experience will be better than most (that is, if you prefer knowledge and wisdom instead of ignorant "bliss" like so many seem to).
The TPMS issue is no biggie; perhaps the batteries in one (or more) of the sensors is bad or they buggered them up when replacing the tires. Let them figure it out and fix it on their dime.
You don't say whether it's a 6M or a DSG; if DSG, I'd make sure the service records indicate a transmission service was done at/around 40K miles.
Being that it's a 2012 model, hopefully you are on a recently replaced battery.
The trunk issue sounds like the typical Mexican build quality/assembly experience, where little rattles are difficult to isolate and remedy. In many cases it turns out the spare tire isn't fully tightened down in the trunk, or other bits are loose in the spare tire wheel well area.
As long as the powertrain, suspension, brakes and body are good, these little niggling issues can be fixed in time (often on your own for free). There's no reason why you shouldn't make it to 300K miles just fine.
Drive more, worry less
