It's because the difference between Chapel/- and Chapel/Silver is much bigger than Chapel/$5 card and Chapel/Silver. The 5/2 vs 3/4 game is inherently unfair for one player, but a $2 cost Chapel makes the difference a bit smaller. This is especially true when you consider that there weren't many good alternative $2 cards in Base, which would make the 5/2 opening especially bad if Chapel were $3.
I suspect that the same argument does not work for Ambassador because Ambassador is weaker in 3p, which is what Dominion was playtested on if I remember correctly. So if you open 5/2, you do not necessarily have to open Amb/nothing. Also, multiple Chapels are generally useless in any deck, whereas multiple Ambassadors are very good in engine decks, so you need to make them harder to pick up with +Buy.