There might be some benefits to a re-engineered ITX motherboard design, but it's mostly constrained by specifications, and cooling benefits would be marginal (I think). GPU placement can be done any way you want with a riser.
I would be more interested in a new high-end mini GPU design, either AMD or Nvidia.
I want a 2080 Ti or upper-range Navi in a ~200mm or less length, true 2-slot card, with a Nano-like hybrid axial/centrifugal design (heatsink fins parallel to airflow from front of case, allowing air to pass from front-to-back). Paint or ceramic-coated copper. And put a good, quiet FDB fan on it (why not source or license it from Noctua, Be Quiet!, Scythe, etc who actually make good fans, not just a cheap industrial fan). Aluminum or other non-plasticky shroud. And no crappy TIM.
Is that too much to ask? ?
(Rhetorical question, don't answer that
)