If I cover a prestige building with another prestige building of the same color, does the covered one still score? The rules seem to say yes but was wondering if I was missing something.
I don't believe so. When you score, you go through 3 steps:
(1) Visible prestige buildings (which only look at visible cards)
(2) Visible AND covered cards (scoring the number just below the cost of the card)
(3) Ramparts (1 point each)
From page 5 of the English rules:
"Each visible prestige building earns Prestige Points (PPs) for all players."
If the prestige building is covered (i.e. it's not visible), it does not score in the first step. Later on, you score the Prestige Points (PPs) for all other cards in the district, which includes the covered cards. For this step, though, the rules state that you score the PPs just below the costs of each card. In the case of prestige buildings, this is a question mark, and so they would score zero points.
The rules could have made this clearer, but I'm 99% sure that covered prestige buildings don't score anything.