I may try a theory if you'd care about reading through...
This has more to do about the pending value of a (to be or)completed building than where it's being built.
The Fertility Clinic is a special case as it is providing Pop-Growth boosting; if you were to hit the buy button BEFORE you had anything properly selected right on the surfaces, costs would remain constantly the same.
But, as you have it focused straight into the project box... it is directly taken into account by the engine so the 'projected effect' can relate to the 'exact amount of hammer requirements' whilst being memorized for direct construction made of cycle_by_turns expenses as usual OR (and this is exactly why cost differs) from a preset figure in Hammers that must be applied to a rush bought asset.
Very complex principle to grasp without a metaphor, i guess;
The architect plans must de drawn before a construction crew goes to the location -- but, the warehouse can still be filled up with all the material necessary for some inventory maintaining COSTS. The longer this stockroom stays idle, the higher heating, electrical bills will get. Until, a truck backups, fills and delivers the products to workers for assembly. The overall spending applied to a finished HQ downtown - is the sum of its parts no matter when (how much for, too) they're accumulated and affected to financial liabilities slot in a statement!
Sort of a Fertility clinic which has yet to distribute phamplets to population wanting to have more kids with specific medical help. But the resources must be kept available by onsite staff.
Serious, that's exactly how i perceive this issue! Game-wise it may just be a lot simpler but call me, an administrative freak.