There are many reasons why the rods must be installed into the correct location.
Here are a few that come to mind:
) Pistons have a front and back, so if you reverse number one and number two rods these two pistons would be facing back wards.
) When re-ringing an engine and installing the same pistons back into the motor, I would recommend putting them back into the same position they were in before.
) When a rotating assembly is balanced the machine shop balances the assembly with the connecting rods in they order they designate them when doing the balancing work.