I just inherited a 3,1 Mac Pro and although I love the beast for what it is, it is ****ing enormous and just does not work in my office. If it was a 4,1 or 5,1 Mac Pro, I would be more inclined to make space for it.
Its hardly news that you're not going make much effort to accommodate a 10-year-old hand-me-down computer (although I don't think you'll have much trouble selling it to someone who does), and you admit yourself that you'd be more inclined to make space for a mere 6-7 year-old one... so that's not really an argument
against a hypothetical 2019-spec tower.
...and, space-wise, what's the comparison? Separate CPU, external GPU and storage units strung together with Thunderbolt cables sitting on your desk, vs. everything in one box tucked away underneath it?
There's also scope for making the old 'cheesegrater' quite a bit smaller and more modern: Probably don't need 5.25" optical drives in 2019 - certainly not two of them - maybe just 2 or 3 PCIe slots (what with TB3, USB 3.1g2 and probably 10Gb Ethernet on-board, they're now only really for GPUs and suchlike). The system disc will be a blade on the motherboard (with room for a second if the machine is designed in reality-land) so that's
at least one 3.5" bay that can be dropped (maybe 2 bays with room for 2x3.5" or 4x2.5" ?)....... but then, on the other hand, this is all going on the floor under the desk, and even halving the size won't turn it into a laptop so why not keep the flexibility?
Besides the technical issues of building a mini-tower with both Thunderbolt 3 AND a removable GPU
There's no technical issue with TB3 and a removable GPU
unless you really need to connect the 1 (one) currently available Thunderbolt 3 display
that doesn't have any other interfaces (other Thunderbolt displays may be available, but they also have DisplayPort and HDMI).
There are cards for PCs that solve that problem (
https://www.gigabyte.com/Motherboard/GC-TITAN-RIDGE-rev-10#kf) via the fugly but effective method of having external DisplayPort cables going to the GPU.
If this is really, really important then Apple just need to treat their AMD life-partners to coffee and waffles in bed and persuade them to make some Apple-edition GPU cards with internal DisplayPort headers that can be hooked up to the TB3 controller - plumbing, not rocket science. If they don't do this already its probably because the vast majority of professional displays use DisplayPort and/or HDMI, and the only real selling point of TB as a display connection is single-port docking & charging
for laptops that are going to be plugged and unplugged daily. I seriously doubt that anybody who is worried about being able to choose their own PCIe graphics card gives a wet slap about Thunderbolt displays.