Are there ways to address this concern or to communicate the value of these unique features to the appraiser effectively—without overstepping?

I read Chad Carson's Small and Mighty Real Estate Investing and I think my path is most aligned with what he calls the "live and fix" method.

Find Brandon's videos on YouTube for the "four square" method of analyzing homes and practice.

Playing the long game, it's not for those chasing rainbows, definently for the LT planned methodical focus. 

Have your attorney send your contractor a letter explaining your dissatisfaction, any legal, ethical, or moral violations his operating methods result in, and making him an offer BELOW your “target” amountbest of luck I have an attorney that I considered speaking with on this matter, but I’m not sure that he specializes in things like this.

They should have good recommendations.If you are trying to do the BRRRR Method, or some other advanced method, now it get's a little more difficult. 

However, it started to get a bit tough since he is no longer in communication with neither me nor the seller and he is living in the house.

If they are, then the enemy method works.

The BRRRR method is tricky here as we've had some of the highest appreciation in the US over the last 5 years.

Did you communicate to them a time frame for this Bee problem to be resolved??