Hey there. My current speaker stands also had foamy/rubbery bits at the corners, probably to prevent the steel top plate from scratching the speaker. I was never quite comfortable with this, so I added blu tak just to keep things secure. Eventually I just removed the nubs entirely, and used blu tak alone, which I found to give a very solid connection. I think this happened before I even filled my stands with sand, so any sonic improvements were probably moot.
As far as marks, I've never seen blu tak leave a mark on anything; I wouldn't try it on anything porous (like unfinished or lightly-finished wood), but it's fine with my (old) DCs and I would guess the same for the i's.
Anyway, MC reported elsewhere good results with BDR cones, points up, between speaker and stand.