FWIW, when the local mill runs my pine off, they start with material that is about 1 to 1 1/8" thick rough thickness. They usually mill this down to standard 3/4" planed on both sides for sale.
For my order they plane it to 7/8" and try to have at least one side planed nicely, and on some of the material there is a minor bit of roughness or mild wane on the one side which I clearly put on the inside of my boxes (I figure the bees are happy in trees so....).
To be truthful I haven't noticed a difference, at least not enough to grab my attention. I do have some hives though, that are propolis machines, almost to the point of being a nuisance to clean up.