This is true of an academy, as well as a Manufactory vs rushing a wonder I suspect. Late game wonders can cost over 1000 Hammers, and while the manual states that some of the most expensive items won't be completely rushable, you will be able to get a near finish. I'm guessing Engineers max at either 750 or 1000 hammers and anything beyond that is left over. Manufactories only provide +3 hammers according to the manual. Here are the building modifiers:
Forge 15%
Workshop 20%
Windmill 15%
Factory 50%
Solar Plant 25%
Nuclear plant 25%
If you manage to get all of those in a city by some miracle given the resource and terrain limits of the last 4, you get +150% which is 7.5 production from a Manufactory, ignoring whatever tile improvement it replaced. It would take 100 turns to make back a 750 hammer wonder rush in the late game, with a Manufactory. That completely ignores the benefit you'd get from having the wonder as well.
A customs house provides +4 gold with the following building modifiers.
Market+25%
Bank +25%
Stock Exchange +33%
Thus it provides 7.32 gold after building modification. We have no idea how much gold will be gained from a trade mission, though my best guess is that it will increase in return based on certain possible factors. Population of city state. Distance from City state. Tech level/era/how many turns into game you are. Unfortunately I have nothing to base the actual return of a trade mission on. If it's 750 gold or later, than again, in the late game it will take over 100 turns to recoup the one time mission with a tile improvement.
A landmark may be the only building worth it as a culture bomb's usefulness is entirely situational. The problem there is that you're giving up something that improves your cities output in a worker improvement, for culture. You're trading food, commerce or production for culture. That's a tough pill to swallow sometimes. On the other hand, a culture bomb does not appear to contribute towards SP popping so a landmark is the only GP action that can help in that way.
Personally I think I might use my great artists for golden ages if I don't need the culture bomb somewhere. The other 3 are always going to do their missions in late game. In early game, a scientist will always be used on a tech. A Manufactury *might* but build early if there's no desirable wonders at the time, though it will probably just be saved. A trade mission depends entirely on the return. If I get a merchant real early and trade missions are under 1000 gold, I actually might built the tile improvement afterall.