As others have said, the M1 has PCIe over TB3. TB3 without PCIe over TB3 isn't TB3.
The issue is the lack of drivers. Some PCIe devices work with generic drivers already built-in to MacOS, others need third-party drivers which will need to be updated for both Big Sur and Apple Silicon. Things like A/V interfaces that need specialised drivers should work once the manufacturers have got around to updating their drivers. Of course, some manufacturers have gone bust, or won't update their older drivers if they think they have half a chance of selling you a new device - but that happens to some extent with every MacOS release.
Then there are eGPU drivers which Apple doesn't currently seem inclined to support at all.
As for things like expandable RAM, SSD and PCIe slots in desktops - Apple have always been somewhat opposed to those, and are unlikely to change. I doubt we'll see PCIe slots in machines below the Mac Pro price level , on-board SSDs have always been proprietary rather than M.2 and the introduction of the T2 as the primary disc controller sealed that. The "RAM hatch" on the iMac has been living on borrowed time because Apple never got round to re-designing the iMac - and I sadly suspect that where machines like the Mac Mini have socketed RAM (that you have to dismantle the machine to get near) it is because it suits Apple's logistics for those models to add RAM after fabrication.
On the flipside, the M1 is Apple's entry level chip for ultraportables - giving it external PCIe or expandable RAM would have been overkill for that market - and if you look at competing ultraportables like the Dell XPS, MS Surface Laptop etc. then a choice of 8GB or 16BG of soldered-in LPDDR RAM and nothing more is par for the course. You can't get LPDDR4 RAM in DIY plug-in form, anyway - and it gets a speed boost by being soldered in with very short links to the CPU. When the higher-end Macs start coming out, I'd expect to see something a bit different.
In a sense, Apple's "non-upgradeable" policy is more defensible when you're getting the speed/efficiency advantage of having all the major components in the same IC package, or even the same die. If you're worried about the penguins - look at the size of the logic board in the M1 Mac Mini c.f. a handful of RAM SODIMMS (...and the extra socketry and PCB area to make them replaceable). Maybe its better to keep the M1 Mini as a working computer and repurpose it than upgrade it - a chain which always ends with a bunch of old components being thrown away.