Except those who need dual graphics cards, and if PCH gets incorporated into the CPU, the new standard for desktops (granted it is a shrinking market) should be mini-ITX. If it were not for the ports people need for devices, Intel might just attach some kind of power connector to the cpu, and just put motherboard makers out of business.
Desktop route point for smaller forms. It is unavoidable and it is not only future = it is already happening.
Just notice how desktop market changed in last decade. First mATX boards emerged from niche and now are mainstream, offering almost as many models as full size ATX boards.
mITX in last 2-3 years are gaining momentum as well.
It all is accompanied by case makers and dropping prices.
ATX is going away. It will be just small niche left for some specific builds.
In future smaller nodes will allow dGPUs to be smaller too. Actually again it is already happening - there are already few powerful dGPUs made in smaller sizes. I think ASUS is making efforts in this field, with smaller custom dGPU boards and smaller cooling systems.
So even dGPU users will use mITX rather than ATX.
Motherboards & ports are not a problem - since even desktop CPUs will be SoC sooner or later - actual "motherboard" will be relatively small piece. Small thing with few ports and maybe 1-2 slots on some % of boards (in new standard sooner or later - much smaller physically than PCIe slots - they're getting too big).
Still all that won't happen overnight. It's slow evolution that will take many many years.
For now ATX, PCH, PCIe, etc are not going anywhere ;p