I am totally not getting what you are saying... Are you somehow saying that the new queen somehow doesn't get fertilized by random drones somehow if you do not notch, therefor you would be stuck with a narrow gene pool or something? I do not see it as a integral part of it to the point of not being able to separate them.
I also do not understand how you are saying notching is a integral part of the OTS system. How do you think it is integral that deep exactly? I like notching myself. I like it because I believe it does help make queen cells and you can make multiple ones on multiple frames for splitting, with greater control.... but OTS imo is to reproduce hives and break the mite cycle mostly (Which is what I use it for, along with dusting with powdered sugar during the down time.) All the new queens are going to go get fertilized by outside genetics anyways on their mating flights, unless you are doing manual fertilization, I've never done it myself.