Its not just the distance from engine to cover but the air circulation and air flow that make an successful installation.
Air inlet for the engine needs to be clean dry air, if you let hot air from under the cover get sucked into the engine, you increase the thermal stress for the whole engine and ancillaries.
Conducted and radiant heat from the engine and particularly the hot exhaust
needs to be removed to outside the yacht via a ventilation system. Taking the waste engine heat from the engine and using the air to transfer the heat will help keep the ancillary items on and near the engine operating at lower temperatures.
One issue with all this airflow is it takes holes or ducts to move the air. Holes and ducts have a nasty habit of allowing noise to travel from the engine to the people around the engine.
I have not worked on small engine installations. On larger installations it was common to start with the holes and ducts first then design the covers to suit. Keep it simple, make sure there is good access to the difficult parts that need to be accessed for maintenance or in an emergency and keep it simple.