Awesome great to get new.
Getting a warranty?
Now is the time to ask for all the "free" upgrades from the bike shop you are buying from.
Ask for at least :
Better tires
Better brake pads
You mentioned the seat so maybe look at a more suitable seat.
IMHO bike shops markup on a new bike is about double .... gotta pay the rent , electricity , employees etc ...
That may be your opinion, but that's not reality. Possibly on the lowest of the low end bikes, but as you go up and price the margin on bikes drops sharply. It's not just the cost of the bike, there's still shipping, receiving, unpacking, assembling, adjusting, and putting the bike on the sales floor. The shop is only (maybe) clearing a few hundred bucks on this bike.
Shimano only makes one compound of brake pad for the brakes that came on the bike. Why would you suggest 'better' brake pads? Heck, it's already been discussed that there are hardly hills where he lives....
The tires are more than adequate for the bike and rider. Getting rid of tubes would be of greater benefit than replacing tires.
And by all means, if you want your bike shop to think you're an *** and treat you like such, go ahead and ask for a bunch of free stuff.
If you want to get on their good side, keep your business local and drop off a cold six pack of their favorite beer just before closing.