The PCI-e standard "PCI legacy" card dimensions are about 5 inches in height. For those slots pictured you'd need 5+ inches of verticle cleareance to get the card out (or in ). For example the middle card there while the slots are fully populated; how does that card get out/in ?
You can rotate it 90 degrees so horizontal in the picture ( and when side cover comes off have far more than just 5+ inches of vertical clearance. However, at this point have up to 3 "flat" card tangential to the vertical air flow blocking the flow ( if main intakes are on the bottom ). On top of that have the blower on each card that manages to grab any of the air that does go vertical and blowing out of case before it can get to the upper half. ( This latter issue is probably still a problem even if have then oriented vertically from the bottom. The cards will attempt to turn the air flow 90s. )
I suspect some liquid cooling fanatics will jump in and say the GPU cards are all hooked to cooling and the heat is simply pumped to the radiators directly beneath the fan. Still haven't actually solved the blocked airflow issue. The cards a still a substantive impediment to getting reasonable CFM ( cubic feet per minute) to the radiate. Liquid is just a "ballon squeeze" in that case ( just shuffling the deck chairs.) .
For those dimensions, 3 double wide slots don't make much sense. Even "front to back" has likely issues at he GPU cards about 9-10" long and the case is only 11". Don't really have much space to put a "blower" to feed the cards in a 'front to back' set up either.
Finally a relatively large power supply would probably negate putting sockets on near the Power Plug in this set up. [ I realize this is simply 'cut & paste' from Mac Pro 2013 model. ( doesn't have ridiculous 8 Thunderbolt ports ). ] A subset of the "blocked" clearance issues here also as to where , even if 'hang' the PS bulk in the middle volume (like MP 2013), what are the clearances from the main logic board below.
P.S. Front to back would easier if used conventional inlets. However, if Apple wanted to continue on the literal desktop 'fever' then could just have two slots. One vertical more toward the middle that doesn't have an outside edge ( video is feed to Thunderbolt and I/O panel ). Another toward the back edge and some cubby hole or door facing up so connections can come "up , out and toward the back". That could be blocked off into a separate thermal zone with air input slots actually over the standard location folks tend to put the fans on GPU cards ( Imagine that actually putting air inlets next to the fan input . .... instead of hiding them 90 tangental to the air flow. ) .
Main thermal area would get inflow from bottom and the random non Apple card thermal zone would get its from the back. Hence decoupled.
Apple GPU hooked to vertical exit fan one and CPU hooked to vertical fan exit two. Again decoupled.
Instead of a clustered "box" of inputs sockets spread them out linearly along the back closer to the rounded corner. The main logic board could be a another thermal zone definer for the I/O chips ( along the "bottom" board whereas the x16 slot is on top. ). Could put a small MBP fan at the top of this "under the board" thermal zone so can pull the 10GbE and Thunderbolt heat out. (only need about 1-2" for that exhaust port so a 1-2" gap between bottom of logic board is probably in zone ( PCI-e card height ~5" + 2" = 7" so have that to work with. )
Probably would need to put the power supply ( or at least the outlet ) toward the bottom back side.
If made the "box" deeper instead of square with height the perhaps add another custom Apple vertical slot ( less double wide because doing liquid-radiators to cut down on need for "double wide" and pack two and have yet another vertical exit fan for the additional "compute GPU" slot.