I thought about it a little more, and yeah, it does make sense why I think late-game count is a little high.
Thinking about supply from population: late-game, city populations are higher, and so they're naturally providing more supply cap simply from the fact that these cities are growing and that you have many more of them. That, more or less, seems like it would be enough, because the larger empire is generating larger supply all by itself. Throw in all the extra 10% bonuses everywhere (Seaport, Stable, Hospital, etc...), and then the effect re-doubles, rather unnecessarily I find. If these values were 5% across the board (from Walls all the way up to Arsenal), it would seem fine to me; and it's not obvious that something like the Pasture needs it at all. The length of game already provides enough supply all by itself.