Dust shouldn't buy everything

Dust is literally nanomachines.  They can reconfigure into almost any structure - and they can be used to process materials at a molecular level, nigh-instantaneously.  Being able to buy entire production queues is pretty much how that sort of thing would actually work.

Dust is NOT simply "money".

If we look at it this way then yes you are correct.

Not everything in the game has to have logical sense but I would still like to limit the instant build options.

You should be able to improve the speed greatly with dust but being able to build up everything at a push of a button seams to much (of course it does cost you it is not for free).