I have a totally different plate (Enduro Guardian) on a different Vstrom (K7 Vee) but I sure get where you're coming from.
Installing the bracket for the rear attachment points was a royal pain. Especially so on the DL1000 of the time, with its lower exhaust run in the way.
Using both kickstand bolts is probably intended to help fight any twisting forces on the bracket. One bolt may be "enough" but given it only has to be done once, I think it's the better approach.
Suzuki seems to be all over the place with protection on these bikes. My '07 Vee came with an absolute joke of an "engine guard." Truthfully, it was no more than a feeble plastic bumper. Zero protection from the bottom, questionable protection from the front/side.
Newer Vees got better coverage, or at least it looks that way, but still short of an actual skid plate.
If it's any comfort to you, I've not seen evidence that the slightly reduced ground clearance did any harm on my Vee. I've ridden some very rocky fire roads since getting the plate, but not found any gouges on the bottom of the plate.
I did have the kickstand bolts back out and the kickstand almost fall off a while later, but that's another hilarious story. :P