With a partly laced wheel, I'm guessing the guys who do it that way find some other way to keep the tool pressed into the notches?
I use the axle nut or quick-release skewer to hold the tool in whenever I'm pulling a freewheel that takes one of the pronged tools. Be sure to loosen it off once you've broken the freewheel loose, because if you keep unscrewing it, you'll break something, as you're effectively tightening the freewheel and tool into the axle nut.