Safety issues.
A gearbox falling on your face is as dangerous lying down as it is standing up
also, more insidiously,
Exhaust gases are generally heavier than air. (of a similar temperature)
so if you lie down under the car, in a trough, with the engine running , expect Carbon monoxide poisoning.... amongst other things
it's less of an issue in a 5-6 ft deep pit, as you're standing up... and your ankles don;t need to breath as much
so ventilation is a MUST.
in many cases, digging the deeper pit wouldn't actually be an issue for the foundations... as you'd be clear of all the support structure....
however, in areas with High Radon levels, , groundwater or other similar issues. there may be other serious risks involved.
including that of your old engine oil contaminating the ground water if you don;t do the build properly, or dispose of it carefully.