The whole point of the expansion card system is to be able to choose which six ports. For all anyone knows I might need six USB Type-A, or two Ethernet and four storage, or a bunch of HDMI or DisplayPort, or what have you; yes, some of these are going to be limited by what the chipset can pump out, but still. That sort of modularity and swappability is something I leverage daily with both of my Framework laptops; that's indeed half the point of a Framework.
And as for the space-efficiency... the existing non-swappable ports are already pretty sparse and spread out. The expansion cards ain't all that big; stacking a bunch of 'em shouldn't take up more space.