Assuming the company is voluntarily hiring them, and not being required by a contract or law that needs an independent 3rd party for auditing purposes, it seems like the pentesting company would do an even better job on the inspection if they had a good chance of getting repair work down the line for every issue they found.

If they make up a bunch of minor things that don't matter, you can ignore those and focus on the important ones. I suppose if you don't have any in-house expertise at all to evaluate what they say, the conflict would be more important?