No you didn't cause any alarm. The passengers door has the same bolt marks and the rear look like the hinge bolt head is within the B pillar.

I talked to the sales guy and he said the CPO warranty would apply and I can bring it in for the service department to mess with.

It isn't that bad but the times the door doesn't close bugs me.

On the other hand maybe I should let well enough alone. There is no wind noise from that door. If this door has been like this for a long time, the seals have mated to the door edges and moving the door could open up an ever so slight gap and then wind noise.

The seals don't look like they have been pinched and could probably handle any adjustments to the door. Adjusting 1/32 at a time would not be much movement.

Sadly doors closing as they are designed is one of my pressure points. :(
SO I am probably musing about this more than I should. Like the CVT on our recent Outback drove me crazy but my wife never noticed. I sit their thinking how could she not notice the put-put-put herky-jerky of the CVT in stop and go traffic??

Bought that Outback in June 2018 and traded in last week on the Volvo. I really like this V60. Getting out of a car that I only owned for 9 months meant I took about a $5,000 hit. But it was worth it!