As you lower the compressor/turbine/MGU-H assembly at the back of the engine it will hit the top of the little clutch assembly. You can move the comp/turb/MGUH 50 mm further back to clear the clutch and lower it further until it hits the shaft between the clutch and the transmission. At that point you need to severely kink the exhaust upward to clear over the transmission. And the space you've lowered the c/t/H into is already very tight because the cars all use inboard transmissions with the gear clusters ahead of the final drive. Also, generally, the more you lower the c/t/H, the more you create an awkward structure on the top of the bellhousing and transmission, and that surface is important for rigidly connecting all the rear suspension and rear wing loads into the engine and forward part of the car.
All ultimately tradeoffs. The Merc/Honda approach makes the engine-rear more tidy, but the front is a packaging and structural mess. The Ferrari/Renault approach goes for the opposite tradeoffs.