I presume your question is what the likely costs are for populating only the BGA or QFN parts on a board that has other components that you want to populate yourself / or leave unpopulated for a kit.
The answer is of course "it depends".
Firstly, there's a big difference between China and "the west". In China, even 100-unit runs are commonly placed by hand (even for reasonably large pitch BGA parts, but anything under say 0.6mm pitch BGA is better placed by machine). This keeps the setup costs much lower. If you end up needing machine assembly, you might as well get the whole board populated because most of what you'll be paying is the setup fee anyway, and there will be a minimum applied for this by any factory. For a 100-board run you are likely to end up with close to the same cost for populating 1 chip or a whole board.
In "the west", a 5-board run with QFN or BGA would likely be placed on a manual machine while a 100 board run would definitely go through a full pick&place machine. Here, for the 5-board run, placing just the "tricky" part may turn out more economical.