I'm sorry, i've looked at the wrong right angle connectors. Those shorter (3cm tall or less) are "down angled 90 degree", i think you were referring to the "right angled 90 degree", which are indeed 5+ cm tall, as you were saying. Sorry for the confusion.
Anyway, i like the current IO design, don't want it changing, it's just the display extensions that bug me. Don't they take out space at the back, in the detriment of the space available for the GPU (its height, to be more specific)? Don't they push a bit further the pcie slot's placement, limiting GPU's height? If yes, then if you relocate them and move the pcie slot a bit more to the back of the case, wouldn't this gave you a bit of spare cable length, enough to move the GPU a bit further down, to allow for bigger right angled connectors, without increasing the height of the case by much? Ofc, this would mean the top should be a removable panel, a cover of sort.
Btw, are you currently using something like these for the extensions? If yes, couldn't the external ports be relocated to the top back panel, in that ~11mm space (placed horizontally)?