Beeswax is a chemical sponge, as Jerry Hayes calls it. It soaks up chemicals and contaminants that the bees bring in or beekeepers are putting in the hive the last couple decasdes. Regular comb replacement is the only soluton. Replacement is not dependent on foundation type. Plastic foundation is easily scraped with a capping scratcher for "crush and strain" harvesting or regular comb replacement.
Small cell and natural cell studies in several states and worldwide have proven ineffective in controlling Varroa or anything else. The spatial relationship changes as bees "regress" so there is no benefit. The bee biology that makes AHB resistant to Varroa is called absconding. AHB leave when the mite load gets high. We are starting to see this with all bees. It goes by another name also - CCD.
Beekeeping is a relative unknown with so many people showing interest and the Internet so willing to show "a better mousetrap" or the "perfect solution" I would put more trust in scientific research than what you can read on the Internet, even this forum, or this post. More thn once I have read ardent seemingly knowledgeable posters here who experience the same challenges a year or two later when they get their first hive.
There is nothing natural about horizontal hives or checkerboarding, but great interest in both by beekeepers in the last couple decades.