I don't think that's the point: if you can ship 16" MacBook Pros with dedicated GPU you could do the same with MacMini; why don't you give me such option? ("you" stands for "Apple" here btw)
desktop grade cpus and gpus have very different thermal characteristics. it quite impossible to have silent + desktop cpu + desktop gpu + very small space.
Putting the cpu/gpu of the 16" MB Pro would enhance the mini greatly. The thermals would be be much better than in a laptop resulting in better performance. Yet, you wouldn't have to pay for an unused screen/battery. Also, while you can use the MP Pro in clamshell mode, it is making the thermals even worse. So why should one get a laptop, if one wants a compact desktop?
Apple's hardware business model is driving margins by bundling unnecessary features in the "trim levels". They don't want you picking and choosing only the parts you need.
I am not sure what you don't understand. There is no way you can cram desktop grade cpu and gpu in such a small space. You could put laptop line of cpus + gpus there which are slower and probably shouldn't be run 24/7 (apples usecase is NAS). Or you put just desktop cpu which has ok integrated graphics already.