One of the issues with M.2 in desktop PCs is how buried from the airflow they are, and often they're literally on the exhaust side of the GPU (many GPUs exhaust on both long edges, and many motherboards just so happen to have an M.2 slot under the PEG) or in the air-flow dead-zone between PEG and CPU cooler.

Overall the AT(X) form factor, with extension cards slotting in at a 90° angle, just doesn't work all that well for efficient heat removal. DHE takes away I/O slot space and requires high static pressures (so high fan RPMs), it works for headless servers, but that's about it. The old-fashioned way of a backplane and orthogonal airflow does work much better for stuff like this; but it also requires a card cage and is not very flexible in terms of card dimensions. The one saving grace of ATX is that cards and their cooling solutions can grow in length and height, GPUs are much taller than a normal full-height card, and many are much longer than a full-length card is supposed to be as well.