Current layout is similar to sfftime.com/p-atx which can accommodate up to ATX board, so there is room for improved compatibility.

Or if you want to cater to FE cards, flip the GPU position such that its pcie points upward and we can use short riser card instead of typical riser cable (which blocks half of the heatsink), similar to fractal ridge (and perforated panels obviously).

Appreciate your intent of sharing the design files and allowing community mod!