Dell Optilex 780 mouse and KB problem

There is a very big difference.

The back ports are soldered directly onto the motherboard itself.

The front ports and/or top ports have to have a cable that connects them to the motherboard in some way.

The extra cable creates another link in the chain that can individually fail (just the port vs a cable and a port).

Performance wise, if there are no failures in the chain they should both be pretty much the same.