I have eight Ruger 10-22's, and some of them have the indent completely remove, by me. The rifles function perfectly well with the bolt handle not captured by the indents. You just have to be careful to hold the assembly by hand during the instal. I removed the indents so I could polish the rod so the handle would ride freely over it during the firing cycle.
I changed two handles to the one that Power Custom sells because it extends out farther and is easier to grab when manually cycling the bolt. I tried the higher power spring, the long one, that Power Customs sells and can't see much difference between it and the factory spring.
There are some really neat bolt handles being made that you might want to check out over on Rimfirecentral. IIRC, a guy by the handle "skeeter" makes them.
Martyn