Rough side in, will promote the use of propolis as a covering as the bees do not like the roughness. Although there have been several beekeepers over the years promoting this practice, recently some "research" types have had a light bulb turn on and started realizing that this may not be all bad for the hive that uses propolis for healthy hive reasonings. Go figure!
Some beekeepers intentionally rough cut their lumber on one side to use the rough side inside th hive.
I do not intentional seek out rough cut lumber. But when I do have it, I will use it.