First, congrats! Is it Marrakesh brown? If so I'm jealous. If not, either way you will LOVE your Alltrack. I like mine a lot more than my previous 3 GTIs.
If you go the oil change route, remember to request that they utilize 5W-40 instead of the new 0W-20 shite ( when I brought my AT in for its first oil change under the "VW Care" package which inlcudes 2 oil changes, I requested the 5W-40 instead. The service manager pushed back, stating that "since this is warranty work by VW it has to be what they're prescribing." I responded that VW's 502 spec still applies to the new engines, they just created a NEW spec and the new ones come from the factory with THAT spec. From a VW/Warranty perspective, they don't care whether you use 0W-20 or 5W-40, as they've ALWAYS required 5W-40 until the 2019MY. The only difference is the 0W-20 nets 3% better gas mileage and doesn't statistically increase the likelihood of warranty payouts, so they went with that for marketing reasons. 5/0W-40 is still the business.
No dealer is going to replace a battery that is functional. You could VCDS it and see what the battery life is like and if it reports poor health you could ASK for a replacement. If they say no, get it in writing. If the battery fails on you in the first year/12K miles they'll replace it for you, since you have a paper trail proving you did your due diligence, they denied you, then the exact issue you were hoping to avoid occurred.
You could wager with them on the alignment. "Perform the alignment. Show me the specs. If it's within spec on all 4 corners, I'll pay for the service. If it isn't, it's on your dime."
Cabin filter... The car hasn't been running much at al so I highly doubt the filter is messed up. They're also like $5 or $10 on amazon for a mann filter so if you want to ask you can, but it's unnecessary and either way wouldn't cost you basically anything. I'm sure they're already not making money on the car, so they're likely not gonna be too interested in eating more expenses. But it's been 400 days, and they've gotta get rid of it. So you do what makes sense to you.
This has nothing to do with the amount of time the car has sat on the lot, and wouldn't be covered by a dealer anyway, but I changed my haldex fluid at 5K just for peace of mind. I've heard too many issues of VW under or overfilling Haldex and DSG units from the factory. Just too important of a piece of equipment that costs too much to fix out of warranty for me to take the "chance" they didn't fill it properly from the factory.