The Mac Pro is far from a flagship product now - it's a niche product within what's increasingly becoming a niche of their overall business. It's an important niche, because you can't develop for iOS on an iPhone, but the Mac niche as a whole is a business that makes up less than 10% of their overall revenue. They sell a healthy number of Macs, but they're not a huge part of their enormous iPhone sales.
Even within the Mac market, their flagship product is the MacBook Pro, followed by the iMac. They don't want to sell a highly configurable Mac Pro to anyone who'll buy something that causes less support hassles and might have higher overall margins due to high-margin Apple-sourced upgrades.
They have always had a policy of pricing the entry-level Mac Pro above the most expensive standard iMac to protect the iMac from competition - they don't want the user to have a choice between all-in-one or expandable, because they'd rather sell the all-in-one. They have often excluded a few very expensive BTO options on the iMac from protection. If you want a standard-performing desktop, you get a screen, want it or not. The Mini is permitted at the low end, with low-end mobile components (and a rare break into midrange mobile components), and Xeon Mac Pros are permitted above the performance of any iMac, as long as they're enough more expensive that they don't compete.
I would assume that at a minimum, a $3699 iMac with the top processor, a 1 TB SSD and 32 GB of RAM is a protected iMac - the Mac Pro will be significantly more expensive than that. There is almost no chance the minimum configuration of the Mac Pro will have less than 32 GB of RAM, or less than a 1 TB SSD - so they'll protect an iMac with those features. They may very well not protect the very expensive options like 64 GB of RAM or the 2 TB SSD.
I would expect the entry level iMac Pro is also a protected iMac, but I'm not sure whether this is so. I am almost sure the protection does not run all the way up the iMac Pro line to the $13199 model - that's a corner case set of BTO options...
If I had to guess, the entry-level Mac Pro will be something like a $6499 machine with a single Xeon SP in the 10-12 core range (and a socket for another - whether or not you can fill the second socket after purchase is unknown). It will have a Vega 64 (or successor) that is upgradeable, but is almost certainly not a standard PC graphics card, probably with room for another. It will probably come with 48 GB of RAM, since Xeon SP is 6-channel), and either one or two 1 TB SSDs. There may very well be room for SSD expansion (4 SSD sockets wouldn't surprise me at all, and more wouldn't shock me). There will be at least 12 DIMM sockets that can accommodate 768 GB of total RAM, and dual-processor versions may have twice that. The port count will be impressive, with at least one, maybe two 10 Gb Ethernet ports, plenty of Thunderbolt 3 ports and probably a bunch of USB-A ports. It will certainly have provision to drive multiple 5K monitors, and very likely at least one 8K monitor!
There are two features that will almost certainly be omitted that will cause a great deal of forum teeth-grinding. One is a double-width, high-power PCIe x16 slot that could support a standard PC graphics card. There will be graphics options, some of them probably very high-end, and there is substantial hope for graphics upgrades after purchase - but it won't be standard PC-type cards, and all the options will be Team Red (AMD). There may well be one or more PCIe slots intended for audio interfaces, RAID controllers or even possibly compute accelerators, but there will be some restriction, whether in hardware or firmware, that will make it nontrivial and unsupported (if not impossible) to stick a GeForce in there...
The second missing feature will be 3.5" (or even 2.5") drive bays. We can hope for (and expect) plenty of SSD slots, but there won't be any way to spin rust inside the case. External cases carry no performance penalty for hard drives (single and dual drives are just fine on USB 3.0 and especially 3.1, while larger RAIDs work over Thunderbolt 3). For VERY large RAIDs with SSD caching that might outrun even TB3, I wouldn't be surprised if a slot supported InfiniBand controllers or the like. External drive cases aren't especially expensive, and everybody needs a different number of spinning disks - from 0 (except for Time Machine, which needs to be external) to 12 or more, so no number Apple put in would satisfy the majority of users (too few and you can't get your storage in, too many and you have a big case with a lot of volume and power dedicated to something you don't need).
Apple is Apple, and they have their own ideas about how things should be done. If your use case includes the words "game", "NVidia", "Premiere" (or other non Final Cut video editor, except perhaps at the very high end) or "media server", they aren't making the Mac Pro for you. Apple has always strongly resisted high-end gaming, probably because of the stability problems games and gaming hardware can cause. They're actively chasing gamers (beyond the casual level, mainly on iOS) away. They have a deal with AMD, they feel burned by NVidia in the mobile chip overheating situation a few years back, and their own software runs best on AMD. They make a direct competitor to Premiere that they feel strongly is better - they may be more forgiving of high-end uses of AVID, Resolve, etc. because Final Cut doesn't have all of the features of those applications. Finally, they have a vision for the future of media consumption, and it's in the cloud, based on iOS and its tvOS relative. They see no need for people to store gigantic media libraries on multiple hard disks unless they're making that media.
I'm not saying they're right or wrong, just that they're Apple, and they think they know best. No amount of wishing for a reasonably priced slotbox to take your GeForces and 3.5" drives will bring the machine they've refused to build for 20 years. The Mac Pro will have some great features, but it won't be the machine some people long for - Apple wants to sell you an iMac, and if you don't want one, you can go run Windows unless you're in a small group for whom they'll support expandability.