I don’t think that they need to make a separate motherboard. Desktops are mainly good if you have a large video card or advanced cpus to use, both of which are either hard or impossible to do when aligning with a libre philosophy, given the current hardware climate.
The state of affairs at the moment appears that librems are still not liberated, they need to support libreboot. The desktop mobo won’t have a stronger gpu or anything of such kind, so you would still be essentially running the motherboard from librems, just with much more wasted space in a huge case instead of a sleek and nice looking laptop, as they are today.
Just get a librem and connect it to a hub in order to use external display, keyboard and mouse, and you got yourself the set up of the next decade. The tower are on their way out for most applications and the ones that need them don’t care at all for free software and just run their restricted intels and proprietary nvidias without a second thought. Hopefully the industry will make a change at some point, especially given the beginning of RISC-V, but we aren’t there just yet. Can’t wait to ditch intel, unless they come clean with the whole ME fiasco, although x86 alone is reason enough to abandon the platform.