So, looking at the example I have given, if there is a stone tool maker present, the bonuses are multiplicative but if the stone tool maker is deleted, the bonuses become additive. Sounds like incredibly messy code to me. And it doesn't explain why a 5/4/5 stone tool maker gives 7 base hammers instead of 5.
besides, in the left hand pane the bonuses are shown as adding up to 65% in the screenshots.
Perhaps the bonuses were at one time multiplicative but were changed to additive, and the code was not completely changed. That would explain the sporadic complaints from players about the AI building incredible amounts of units. If you have a bit of feel for maths formulas, you'd know that a multiplicative formula like (base) x (1 + bonus1) x (1 + bonus2) x (1 + bonus3) goes up extremely fast as the bonuses get higher, much faster than an additive formula like (base) x (1 + bonus1 + bonus2 + bonus3). Write out some examples for yourself if you don't believe me.
Like I said, the city bookkeeping is in need of a thorough audit. And if the bonuses are indeed sometimes multiplicative as you suggest, the code should probably be thrown out and rewritten, with bonuses being additive as the norm, as this is much easier to balance.
Any discussion about unit cost and game balance is meaningless as long as the city's bookkeeping is this buggy.
They add up to 65% but its not how engine counts them that why they each have separate line, its just city UI show things for us in a confusing way, every new source is separate multiplier for game engine. Not saying it is good or bad, but it is how it always was in civ4, no other mod pushed game engine this much like C2C so none paid much attention to it.
I love that every new line can be multiplied like that, its very easy to scale things with each new era. Every era could rely on new multiplier layer to scale things up quicker. But that is discussion for another time.
What happens once you remove building or recalculate is odd for me too. But after you do a turn it get back to how it was before. Might be just UI messing up or some calculations updating only on turn calculation. Or it might be that some bonuses get multiplied for each building, then base summed up and it gets multiplied again

Or some buildings that gives bonuses from tech unlocks or resources give them without unlocking or obsolete bonuses not take out properly.
AI building so many units is not really an issue, I for instance grow my wonder capital to size 200+ regularly, with slaves, wonders and all buildings built i churn 15k hammers a turn if not more, and that is normal for me. I get really upset that in modern age i can only build just few units a turn, or wonders take too many turns to build, feeling when you build 40 prophets at once is really satisfying

Production output to building/unit costs falls of drastically with the era passage, that's when game becomes boring. Need to up production a bit in industrial/modern era, falloff is crippling.
Pick from my test game, industrial era, pushing for new tech unlock. My capitol makes more research than any AI with all his little villages
