I think there was a rush during the early Intel transition because they were dirt cheap computers you can upgrade yourself and even dual boot Windows. I feel like there was another big bump for them as a set top boxes to run XBMC or something. Might be wrong though. M1 release also saw the Mini's be a cheap entry point to seeing what Apple Silicon could do.
The first Intel Mac minis came out in the era of Front Row, Apple's attempt to turn every Mac into a media center computer. They had IR sensors and remotes. I had one hooked up to my TV, which was a big step up from the first gen AppleTV.
Plex started as a Mac-only XBMC fork during this era. There were also apps like Remote Buddy which let you control pretty much everything with the simple remote that came with the Mac. Apparently Remote Buddy still exists and works with the current gen Siri Remote.
I was happy to see that x64 mini computers have really come along. Some of the units from China are really impressive with some exposed full PCI-E buses.
Arm64 is still limited for sure, but with Snapdragon and Windows finally committing to ARM I think the future is bright for that. Just not here yet.
A thunderbolt 3 connector is 4 PCIe lanes, isn't it? I know there can be compatibility gaps, but there are definitely TB-connected enclosure boxes available. NVMe connectors are also 4 PCIe lanes, and I believe any of those can be broken out and used for whatever (m.2 cellular data modems for example).
Are you thinking of plugging in actual consumer expansion cards, or are you wanting the lanes broken out on some kind of riser where they can go to hardwired stuff on a carrier board?
Thunderbolt isn't literally four PCIe lanes; Thunderbolt can encapsulate and carry PCIe traffic, and Thunderbolt controllers are typically connected with four PCIe lanes, though the amount of PCIe traffic a Thunderbolt link can carry is not necessarily as much as four PCIe lanes.
Directly exposing literal PCIe signals cuts out the pair of expensive Thunderbolt controllers.