Why compare a box you had a few years ago to the new Mac Pro? Today you can put amazing performance in mini itx or micro atx cases.[1] Granted Apples custom design still offers some space savings but also zero upgradability. Of course those small standard cases aren't made for xeon CPUs and Dual GPUs, but most people that buy/need powerful workstations do not really care about the size of the thing.
I get things are better now. I type this on a 2013 Macbook Air. This is my main, personal dev machine. I understand the levels of improvement we have achieved.
But Apple has a truly novel design with the new Pro. Even the machine in your link has 1 CPU fan, 1 GPU fan and a power supply fan. And it's still quite empty and not that small. No one except Apple is even trying.
Depends what you mean by upgradability, my main dev and gaming rig is watercooled. It is so silent the only noise detectable is the spindle HDDs.
I can slam in another PCIe SSD RAID next year and hopefully get rid of those too.
The Mac Pro of course can't slam in a PCIe RAID, you have only thunderbolt, which isn't as fast as a 16 lane. You have no ability to choose graphics cards made by third parties, my box just has reference design ones, with ek blocks on them for the cooling. Of course this means changing the graphics card takes 1 hour, then letting it "leak test" in the bathroom for a night. I would still say it's upgradable, but clearly I've traded ease for silence and performance (you can generally get very reliable over clocks with such cooling).
This is why people complain it isn't upgradable. You can't easily put in anything you want, it has to go external, which is fine for some, but abhorrent for others. The options of what you can upgrade are entirely a single vendor lock-in. Some people dislike that. These people (such as myself) like to have a free market of competition and innovation on every component available.
Being able to replace the PSU, GPGPU, 5.25" drives and 3.5" drives is upgradable. Expansion will have to be entirely done through external PCIe chassis, and TB2 is NOT as fast as PCIe3. It's such an inelegant solution and very half-assed.
I don't just want an engineering marvel on my desk. I want it to be pragmatic and easy to expand. Using the excuse that most machines are going the other way is not viable – this is a professional machine, and every professional has different standards.
I think you hit the nail on the head. This is a professional machine, and the professionals it is aimed and, that are going to be buying this machine, are not interested in upgradability in the sense you talking about.
Find a good price/performance ratio, buy and use machine for 2-3 years, sell and buy a new one. The fact that this machine houses all the components you want to upgrade inside of it (CPU,GPU,RAM,PSU) and all the components you want to keep outside (NAS/RAID primarily), makes this prospect that much better, less waste.
Not to mention the usually excellent value retention on Apple hardware makes this a pretty darn good investment. Again, if you are in the target market that is.
[1] https://teksyndicate.com/videos/build-most-powerful-mini-itx...