While I personally drill and tap either 1-72 or 2-56 holes for mounting Kadee's, there is always more than one way to get things done. Lots of tricks out there, as mentioned, each with some considerations for the modeler.
It's awesome that companies like Lionel and MTH are including Kadee gearbox mounting pads on their newer tooled equipment. I wish atlas would move away from their larger gearbox and either make a scale gearbox or use a standard kadee gearbox. Hate to see such a large oversized gearbox on incredibly detailed cars like the Trinity 5161.