I guess this is more for systems with integrated vodeo? Or Threadripper/Epyk systems?
Pretty much - same problem with a lot of boards limited to ATX dimensions, i.e. 12" x 9.6". Unless you limit to two DIMM slots, there isn't room for something like ASUS' DIMM.2 solution, and there isn't room to put a lot of M.2 slots between the PCIe slots too.
But then, you get only a single current-gen PCIe x4 slot that's separate from the 16 lanes dedicated for the GPU. So a few manufacturers have been providing cards to do two M.2 NVMe drives in that slot. And surprisingly, the higher you go up product stacks, the fewer extra x1 slots you get - and fast, judging by Z690 ATX boards. Anything other than entry level (and Z690 isn't entry level, I know) is limited to those three slots, the primary x16 slot, a second x16 slot that takes eight lanes from it (so they become x8 / x8), and the independent x4 slot.
Additional quandary on the soapbox - if your board doesn't have Thunderbolt built in, then it might have headers for it - and you can spend another ~$100 to put in a card in that x4 slot. Or if you need >2.5Gbit ethernet, well, now you need to use that one slot for a network card.
And then you hope you have enough M.2 slots for the storage you need, or SATA ports that aren't disabled by using all the M.2 slots.
That, and then AMD decides to abandon HEDT as a step above their consumer / business line - and we have no real word from Intel if they're going to continue their HEDT releases.