I have "incubated" ripe cells in many colonies, Qr ones, but I use the top super preferbly with three supers so there is a two super buffer between her and the cells.
One has to remember that the bees know best, and in the process of producing cells, and for that matter the end result of queens, there will be losses.
From say 20 accepted grafts there are likely to be 16 odd cells produced, and if they are at the open stage given to a Q right colony they will finish them off and keep them through to hatching in cages. However there will be losses so if you end up with 14 or even 12 virgins you are doing well.
After mating then 10 good queens is a good result. It pays to kill any that seem in any way inferior. Better to take the loss at that stage than risk a main colony.
PH