So it looks like you brought in a bike for service and they fixed it for not a ton of money but of course like all shops these days are super busy and have their own protocols for dropping off? Any shop should look at the bike holistically and make sure there are no issues most customers don't always see problems it is why you hear so many squeaky chains and we see so many people having no idea why they aren't braking when they have zero pads left. Plus if they give you a proper estimate you can approve that so you know how much it will be before you complete the service which is quite reasonable.

I will agree it is good to support the mom and pop shops but it doesn't look like Trek did anything exceptionally wrong in this case. Maybe they seemed a bit annoying on your end and there were some crossed wires but it doesn't seem like they overcharged you dramatically for a tune up and a new chain. The average tune up is going to be probably $100 and a 9 speed chain is $25-45 plus you have tax so over all not to terrible plus if they didn't remove drivetrain components for the tune which is probably the case they would have charged to install the chain.