The Rio is grounded to a separate grounding point in the trunk, where the MTX is also grounded.

The Rio harness and the Sony are both grounded to the original grounding point of the stock Bose HU.

The above statements contradict each other. Which place is the Rio grounded to? The stock wiring point or the grounding point in the trunk? You say Rio twice. Which is it?

Anyway...

Remember the following:

The electrons are going to try to take the easiest route to ground. If you have a tiny skinny little wire grounding the head unit (ie the factory wire), and a fat wire grounding the amp, the electrons might choose to go down the RCA cable to the amp.

Conversely, if you have a crappy grounding point for the amp in the trunk (for example, you've grounded it to a strut that is spot-welded in place instead of to the floor pan), then perhaps that ground is less good than the one for the head unit, and the electrons are going to go up the RCA cable to the head unit.

At any point, if there is a loose connection or a cheap piece of wire, then that's going to be your bad ground point and that's going to cause noise.