To be pedantic, the air intakes were not moved, they're still in the same place up high behind the cab, that's the engine intake.
Exhaust wasn't the problem, it was the heat which as we all know from physics heads to the top of an enclosure. The problem was simply that the engines could not get enough cooled air over the radiators.
The radiator intakes are normally also at high level and vent out through the fans on the top, but they didn't work well in SP's long and numerous tunnels over Donner, often overheating and shutting down; that put extra stress on the remaining engines and in a domino effect several would fail and the train stall, not good if the manned helpers were stuck in a tunnel.
To overcome this SP trialed 'elephant ears' on standard engines, these worked by shielding the intake from the hot air near the top and dragged cooler air from lower down near the walkway. Two classes received elephant ears, SD45 and GP40X
The SD45 comes in two versions, round top and angular.
Australian Pacific National XR class still have them fitted....or did until recently.
The trials with the elephant ears were successful, so when SP and DRG ordered new SD40 & SD 45 EMD revised the design to move the radiator intake to low level near the walkway, they also revised the radiator placement and moved it above the fans; thus, tunnel motors were born.
The GP15 also has a low level radiator intake but that's not for tunnels, the rad core follows the same design at the tunnel motors where the fans are below the radiators, therefore the traditional waffle intake won't work.
One other type of radiator cover was fitted to some GE U boats, both SP and ATSF had them, these are not engine intake shrouds but sound baffles as the fans were too noisy.