[ref2coach]

3-4-5a States "only one visible manufacturer's logo/trademark/reference is permitted see 3-6-2 for size requirements".
3-6-1 states "On visible manufacturer's Logo/trademark/reference or school logo/mascot is permitted on the wristbands, headband and compression shorts."
3-6-2 "Size shall be limited to 2.25" and shall not exceed 2.25" in any dimension on any item.

Uniform shorts with a 2.25" Manufactures logo AND a Team logo ~4" x 4", would or would not be legal?

I say not legal.

I have been told that since school logo is not specifically prohibited in 3-4-5 and shorts/skirts are not listed in 3-6-1 that there is no limitation on the existence or size of a school logo on the shorts/skirts.