When I worked as a radio tech, we always mounted antennas directly through the roof in order to avoid such problems. Normal position would be in front of the roof rack. Often straight over the domestic light, to make things easier. If mounted with care, with a quality antenna and a non-acid sealant, it would last as long as the rest of the car.
Only if a car needed a temporary comms-radio for a day or a week, we would mount the antenna on a bracket on the gutter or rail, and it would work good enough for a day or two. Or use a magnetic mount.
I've never done it with a cross-bar on roof rails, but it should be possible to get enough grounding for the antenna up there to.
Whatever you mount the antenna on which is not considerably bigger than the antenna, will act as a part of, and an extension to, the antenna.
For grounding, when it comes to radio waves, one can not think in terms of electric grounding. It is not the same. Good electric connection is not good connection for the signal to the antenna. Think area -- the wider the ground straps are, the better. So for a roof rack/bar, I would connect each end of the bar (or each leg of the rack) to the body of the car with a wide copper strap, while ensuring good metallic connection at each end. Now this is not very practical on a car, so one has to compromise. If, e.g, you use several small straps spread apart, it is nearly as good a a single strap with the same width as the distance between the two straps furthest apart. Which ever way you try, make sure both ends of the bar is well grounded.
One practical way could be to hide the ground points inside the brackets of the bar and rails. Thinking of the rails of my 100: The feet of the rails are fastened with small bolts into the roof structure. If we add some tooth lock washers, it would be good. Next, the rail-foot is made of some kind of alloy which doesn't connect very well to the steel tube rail, so a stainless screw/bolt with the same toothed washer could connect the two parts. Then comes the bar to rail connection, which is normally by a clamp with a rubber sleeve. Now, if we get some kind of spikes in between the clamp and the rail, that penetrates into both, several at each end, it could work. Some kind of sealant would have to be added to prevent corrosion. Something similar between clamp and bar? (Can't see how they are joined right now) --- This could be my aproach if I had to mount a GP antenna on a roof bar.
Still, the bars and rail would be a part of the antenna; but the biggest problem is if they are only partly part, because of lacking or bad grounding -- some kind of floating disturbance between antenna and ground.
This is written as an attempt to provide better understanding if the problems regarding the mounting of GP antennas on vehicles. If you look at the lcool site, they have quite a bit of info. The aussies have more experience in this matter than most.
Good luck, and keep us posted
