Well, that's good and I'm glad we've got someone with expertise to ask. However the question refers to the static state. The beginning point if you want to think of it that way; how is the bike was before the rider compensates by his own placement. Does the advantage generally go to the bike with the farther forward center of gravity?
Assuming we're talking about two bikes of the same model, and we're talking about how well the bike is going to corner? Most likely. In the words of Randy Illg of FrameCrafters: "These old bikes were designed to do everything. Carry the mail, ride to work, two up touring, bring along the dog. If you want them to handle you need to make some changes."
How about its height relative to the road or the axles? I would think these things have a measurable and measured effect on handling.
You would think correctly. It is entirely possible to make a bike handle much, much worse by making bad choices. It makes me cringe every time I see someone put a 16 inch rear and a 19 inch front on thier "cafe racer." By lowering the rear you are increasing the rake on the front. Making your bike corner like a bus.
As to forcing more weight to the front and 'planting' the front wheel, is that accompanied by an equal uprooting of the rear wheel? One presumes there is a trade off. Do you find this to be the case and if so is it bothersome?
Keep in mind that these bikes we're talking about tended to be pretty rear end heavy to begin with. By moving some weight forward you aren't hurting anything. And you can keep the rear end under contol by applying weight to the footpegs.
If I may be permitted a brief divergence? Consider dirt bikes. Very tall bikes, right? But their riders go around corners just fine. While standing up! That shouldn't be possible! By standing up they've raised the center of mass of the bike/rider unit very high, maybe brought it up a foot or two. Why don't they go screaming off into the haybales to die in a flaming wreck?
Because center of mass doesn't matter as much as where that mass is applied. A seated dirt biker may have a lower center of mass but he’s applying that mass in the wrong place, high up on the bike. The standing rider may have a higher overall center of mass but he’s applying his mass down low on the pegs where it will do him the most good.
Back to your last two questions: No, I have not found that the bike feels “uprooted” in the rear end with the changes I’ve made. You could make the argument that by raising the rear to quicken steering you are making the bike less stable in high speed, straight line situations. I personally have not found that to be the case at, say, Road America or Daytona. If I did feel that to be an issue I might lower the rear using the adjustable ride height feature of the Ohlins shocks or I’d put on a longer chain and run the adjusters all the way back to increase the wheelbase.
Keep in mind that I don’t have any formal education in this stuff. I’m just a guy that like to ride motorcycles. And who currently has a lot of free time without access to his shop.