Hmmm, both locations have their pros/cons. One advantage to the hood-mount location is the driver can immediately tell if the antenna will get hung-up on a low profile entrance (garage, carport, fast food drive-thru signage, or low hanging tree branch, etc) and can quickly stop before impact. The rear-door location is totally hidden from the driver's view for any advance clearance warning (until it's already too late). The hood-mount location is on the same side as the hood-support rod, so the antenna really won't interfere with any under-the-hood engine maintenance that the hood-support rod already does.
The rear-door location does look more "traditional" for an off-road vehicle (like Jeep's have done for years on that corner location). Plus, the antenna propagation would be better as the VX's roof ground plane would focus towards the left-front reception pattern (great for advance Smokey-The-Bear reports on the freeway, and to stay in contact with convoy leader). Trying to hide the long cable-run may also pose some interior challenges with carpet/body panels. If you decide to go with the rear-door location, try to slightly bend the bracket or use some sort of shim, so the antenna is a perfect 90-degree vertical angle and not leaning to one side.
Either method would work. You'll have to weigh all the pros/cons and see which one would work best for your lifestyle. I concur with you that drilling a hole in a body panel/cladding might make the VX bleed. Just my 2-cents.