dropping a carpet into an empty lower class bunkhouse will push its quality to "great" satisfying that upgrade requirement. Adding cots will then lower the quality and that bonus will go away. But what happens if you accept the new colonist before dropping the cots?
I've done exactly this (sort of, I expanded some bunkhouses, and then dismantled some cots so I could install them in a different building) - in the short term, you'll simply have excess colonists (the population tool will read, for example 11/10 labourers). That situation didn't last long, since I was already building new housing, so I don't know what the long-term ramifications might have been.
