Yes, I've had the same thought. I'd like to build a PC-compatible motherboard, but I want just a little more kick than Sergey's XT. Even at 9.54Mhz, just doesn't do it for me.
Reason for not making newer boards is probably an inability to track down chipsets in reasonable volume, coupled with greatly increased complexity. I know very little about such matters, but basically the AT is a more complex layer upon the AT which requires more BIOS code and support circuitry. The XT was a simpler machine, more in line with hobbyist SBC efforts.
There were boards without chipsets into the 386 and even 486 era. Mostly very early, very expensive boards with limited functionality and performance. They would fill an entire full AT board with chips just to achieve core functionality and perhaps DIP RAM sockets and a cache controller. These probably used rare, hard to obtain chips for some functions, were highly complex designs, and would be beyond the ability and budget of most hobbyists to build.
Here's a picture of such a board.
https://www.ebay.com/itm/VINTAGE-386-MOTHERBO … r-/312926027673
Also, doesn't the NuXT use a rare thirty year old XT motherboard logic chip, the FE2010A? In a sense, it's not so modern -- if it were, it's be running at the much greater speeds later NEC embedded 8088s attained.