What if there were duplicates of each facility which had its own upgrade path that stopped at whatever level you wanted? This would also solve the problem of multiple facilities upgrading to Cultural Center, as there would be duplicates of that as well.
(I can't remember the Proportions names so I'll use the SE2 names
)
Outpost A (non-upgradeable)
Outpost B -> Colony B
Outpost C -> Colony C -> Settlement C
Outpost D -> Colony D -> Settlement D -> Cultural Center D
Spaceport Outpost A (non-upgradeable)
Spaceport Outpost B -> Spaceport Colony B
Spaceport Outpost C -> SpaceportColony C -> Spaceport Settlement C
Spaceport Outpost D -> Spaceport Colony D -> Spaceport Settlement D -> Spaceport Cultural Center D
Of course, the upgradeability of any facility would be determined at build time, but at least it would work better than the standard system... And it would have the added advantage of keeping all the levels of facilities on the screen without turning off "latest only"!