I've had this on two bikes. I suspected that it was NOT wheel dish because, like yours, the wheel was centered in the chain stays. I checked dish and it was good. I checked frame alignment using the string method, and it was good.

With the frames stripped down to bare naked I discovered what was wrong. Setting the frame on a known flat surface, it would teeter-totter. Meaning, if the bottom bracket was flat on the deck, then one dropout would be touching the deck and one was a few MMs off the deck. If I pushed both dropouts down to make contact with the deck, the bottom bracket didn't sit level. Upon further and closer inspection, and measuring, I could see that one dropout was positioned and welded into the stays slightly higher than the other. I confirmed this by measuring chain stay heights with the bottom bracket flush and level. It was just the dropouts.

These were cheap bikes so my solution was very easy. I took a file to the "low" dropout. Removing a tiny bit at the dropout has a much bigger affect at the top of the wheel. Got it sorted very quickly, easily, and it's not visible because the QR or axle nut will hide the work.