I have never seen a queen in a queenright system get up through the excluder from the bottom box.
I have had the odd virgin emerge early in the top box tear down cells and it is a pain to locate a virgin queen which has the run of several boxes above the excluder.
I work it the same way as Jim rotating brood from the bottom box to the top box every 10-14 days.
Getting back to the original query, I don't think it matters if the cells develop in a queenright cell raiser, finisher colony or incubator. The trick is to do the transfer as late as possible to avoid chilling.
If you hold a cell up to the light you can often see movement inside and then you know for sure you are not inserting a dud cell with a dead queen/pupa inside.