2006 regulations concerning your question:
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5.4.3 The crankshaft centreline must not be less than 58mm above the reference plane.
5.5.1 The overall weight of the engine must be a minimum of 95kg.
5.5.2 The centre of gravity of the engine may not lie less than 165mm above the reference plane.
Which means:
- it is not the engine that must be of minimum heigt above the bottom of the car, but its crankshaft. Changing the design of an engine to lower the crankshaft and thereby the CoG is therefore useless (and if so they should raise the engine higher from the ground to comply with 5.4.3
- The CoG is a physical term that is the point through which the force of gravity seems to act (the balance point). While it is beneficial to lower that for the car's cornering performance, it is now limited to be at least 165mm above the car's bottom. This means in effect that adding mass to the engine (since today's F1 engines could weigh a lot less than 95kg) cannot be done all at the bottom as it would lower the CoG too much.