Well, you'd have to check how many PCIe lanes you had free - there's a limited number and Apple have used up quite a lot by including 2 Thunderbolt controllers (for 4 TB ports). I'm not sure that's the reason on the Mini (which doesn't spend 16 PCIe lanes on a dGPU) - but you'd need to ask someone who actually understands motherboard design and the technical details of the Intel chipsets in question.
However, although the Mac Mini case was originally built to hold various permutations of spinning rust, SATA SSDs and optical drives, past Minis have used mobile CPUs - I think this time round Apple have filled the available space with cooling gubbins so that they can use desktop-class CPUs. Finding space for M.2. might be tight - making it user accessible even harder.
Of course, nobody held a gun to Apple's head and forced them to build the new Mini into the old box designed for the optical disc and mobile CPU era - they could have thought different and designed the whole thing around user-accessible RAM and SSD - but tooling up for those solid aluminium cases costs money.
...which brings up the final reason: a user-accessible M.2. slot would mean that Apple couldn't charge 3x the going rate for SSD upgrades - and since they charge a similar mark-up on bog standard RAM SODIMMs there's no reason that a non-user-accessible M.2. would lead to cheaper upgrades.
I think the point of the Mini is that, if you need substantial storage, you'll keep the super-fast internal SSD for system/apps/temp and get one of those nice matching 3rd party external drives designed to stack with a Mac Mini that were readily available until... er... oh, wait, until Apple released the underpowered 2014 Mini and then let it wither for 4 years and killed the demand. Still, they'll hopefully come back (in Space Grey and loaded with TB3/USB 3.1g2 goodness) now.
The 256GB SSD is probably the "sweet spot" - my main beef is that the 128GB on the entry level quad core is a bit small even for system/app/temp if you're talking about "pro" apps (if you're going to justify the $300 jump over the previous Mini by it now being "pro").
All three CPUs have x16 PCIe lanes, with x4 times 2 Thunderbolt 3 controllers, so that eats up x8 lanes there and at least x4 for the NVMe storage, although because to the way Intel advertises hows it allows the OEM to carve up the lanes, I think Apple has to use the remaining x8 lanes -
https://ark.intel.com/products/134905/Intel-Core-i7-8700B-Processor-12M-Cache-up-to-4-60-GHz- - which I suspect they use anyways with the T2 chip versus x4 previously, which may have allowed Apple to add the HEVC Transcoding (which I suspect is just a link to the QuickSync hardware in the CPU), while the 300-Series chipset connects to the CPU via DMI 3.0.
Taking into account the 4 Thunderbolt 3 ports, adding a dGPU would have eaten the other x8 lanes of PCIe as it does with the 15” MacBook Pro, forcing the T2 to run storage through the DMI 3.0 bus from the chipset to the CPU, which I really would rather it not do even if that means running an eGPU via a Thunderbolt port. Storage has almost always been my priority, even over GPU, because even weak CPUs can benefit from super fast storage storage as up until recently, the market has not seen those kind of storage speeds being shipped by default, at least not on the PC side.
No, nobody held a gun to Apple’s head to use the same chassis, but a Mac mini would not be a mini if it was made much larger and I am not even sure we would have gotten a new mini if it meant new CNC milling, instead of simply re-painting the existing chassis. It won’t surprise me if this was a condition of developing a new mini.
A user-accessible M.2 slot would mean that there would be no T2 chip in the Mac mini as Apple created its own SSD controller. Besides, giving users the option of adding their own m.2 is a bad idea all the way around. Apple would never allowed that to be used as a system drive, it that would be a recipe for disaster given the relative newness of APFS and the different levels of NVMe storage out there that would give disparate experiences. Intel makes great SSD, but a 600p NVMe doesn’t give very good Write performance. On top of which, Apple would need to write the NVMe drivers to work with the different controllers that exist. No one would follow Apple’s recommendations on what to buy and what not to buy, resulting in more tech support calls, inconsistent experience and the real possibility of data loss. Doing what they do now lowers that possibility dramatically and ensures a consistent experience speed-wise.
Yes, Apple charges too much for their upgrades, but it is not 3x too much, not given what Apple is trying to do with storage and the T2 chip.
