I never considered the prominent numbers in the game as being, or needing to be, realistic.
Absolutely. All numbers in the game be it income, building costs, research costs, ship costs, everything are merely arbitrary values that have been "tweaked" over time into a working relationship to each other that basically makes sense.
There's no relationship between anything in the game and real life, nor does there need to be. It probably would make more sense if everything was in terms of some abstract "unit" like income unit or production unit, etc. Why they chose the units of income to be billions of credits is most likely because that's a reasonable range for a plantery economy just like initial planet populations in the range of the 6B we have on this particular planet.
As far as then how a single "building" like a manufacturing center requires 3 bc of maintenance that's just the value that makes it work in context of the game. If it bothers you to think that the maintenance of a single building is so high then consider it like Willy said as a manufacturing complex covering a significant percentage of a planet.
Any game is going to have "holes" in it's logic that requires the player to have a minimal ability to suspend disbelief. It is just a game after all.