I beleive that in a new sax the ideal situation for making key mechanisms work properly is to have all of the keys in a stack as close as possible follow a line so that the key heights over the tone hole can be adjusted more easily and lost motion between keys that articulate can be kept to a minimum or elliminated. Not nessesarily fall in the same plane as suggested by the OP.
In an instrument that is being repaired for having unlevel tone holes, the repairer must determine the cause and the best plan of action before doing the fix. ( I think the do no harm moto is a good one) All too often I see instruments that the person doing the previous repair decided to take a file to the tone hole without removing the dents around the tone hole. This in my opinion might be fixing the problem at hand but is doing the customer and instrument a disservice. Later on when the customer decides to have the instrument more completely repaired, body dents/ bends removed and repadded... the tone hole will be unlevel again and in addition to that there will be less material and possibly enough change in tone hole height to affect the pitch. So, with that said, for the sake of future repairs and maintaining the integrity of the instrument for future repairs, IMO it is better to leave the files and tone hole finishers in the tool box, if the customer is unwilling to have the root cause of the problem fixed. If you are a newbie un skilled in the art of dent removal wanting to do a repad on your sax or a seasoned pad changer that never got the hang of pushing metal around, leave it alone! Shim, add glue, bend pad cups, but don't "Level" the tone hole because you are just damaging the instrument for future repairs.