Figured I would just chime in. I've been debating whether or not to go with just a JB4 tune for the past 3 years. I have heard of cases where people just running JB4 tunes were denied warranty service even with the unit removed, while that does not seem to be a common issue, it does happen. If they suspect the car was running modded, despite no TD1, I am sure VW will do all they can to try to find a way to screw you out of warrantied work. Yes the 1.8t is a proven robust powerplant, but that does not mean it cannot fail. I would say proceed with caution, and if you decide to go through with power mods, don't expect VW to have your back on anything. Warranty work on things not affected by power mods should be covered by warranty but you may have to fight for it. If this is your only car and you do not have the option of working from home, I would really think about that too.
Before my Alltrack, I had a b6 A4 1.8t, that for the last ~20k miles I had it, was APR stage 1. It was a somewhat high mileage car, sold it at ~185k, no issues at all with the engine/trans. I made sure to follow all preventative maintenance, oil change every 5k with quality oil, but I also young and drove it like I stole it 24/7.
I know these cars are slow/boring when they are stock. Its really tempting to get it livened up a bit. I am just waiting until I don't have a warranty to worry about losing. Most people seem to run their cars modded with little to no issues. I would just say, don't rush into anything, proceed with caution, and don't do anything you cant afford to fix out of pocket. Just my 2 cents.