I need GND on the roof but want to avoid a GND wire from the engine compartment going up to the roof. Unfortunately the roof rails ('04) are not grounded.

 

Shouldn't be too hard to ground them, no? Well, assuming pulling down the headliner doesn't phase you. How much current are you planning on passing through them? There are plenty of ground opportunities already there like sunroof motors or cabin lights.

 

About 10A. I had the headliner off recently, I don't like to got through that again. I don't understand why the roof rails are isolated.

 

10A is a healthy amount of current. What are you powering, and what else is up there? Is it all stock stuff - sunroofs, lights? Or do you have antennae or other sensitive things?

The problem with sharing a ground is that if both devices fed by that ground are "on" at the same time, then they will interact with each other. Depending on what those things are, it could make a big difference - or none at all. Not knowing any more than what you've already shared, I'd tell you to run a dedicated ground unless, maybe, you can tie into the body metal. Even then, I'd be paying attention for possible changes in performance of the old devices as well as the new.