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?
If you "want" a mid-level "box with slots", that's going to be bigger anyway.