Oh yeah, that do depends on the size of the system, manpower available and thickness of the substrate. If there is a 100mm sand level, in a 700L tank, rather remove it as it will just then be too heavy to get enough guys around the tank to lift it. Especially where you need to go through a narrow doorway.Keep most of the water as possible. Leave the substrate in the display covered by about 20mm water.
So yes, these are all guidelines, but adjustments needs to be taken depending on your circumstances.