Second follow-up update! When I posted this issue a few days ago, I had ordered a third party post-flat adapter from Amazon, but I didn't think it would have resolved my alignment issue. Anyways, after posting my first update the part arrived 30 minutes later and I decided to install it. Amazingly, the new adapter appears to put the caliper closer into alignment (just barely though). I'm not sure if the Shimano adapter was perfectly in-spec or this no-name adapter just had more leeway for sloppiness. It appears to have resolved my rotor rubbing for now. Thanks for all the help!