One thing to note about the clearance drill size, and those that think it's too big. A std size clearance drill/counterbore is not designed to locate. Dowels/taper/roll pins are for locating, and the capscrews are for fastening. If you need a screw to do both, you must accept that there will be reduced accuracy, and repeatability, and you should use a flathead capscrew/countersink. Std counterbores sizes, are great when you're laying out all the hole locations with scribe lines and punches, and drilling them in a drill press. Sometimes the extra clearance comes in handy....
Susquatch, your method is fine. There are many ways to skin the cat. Drilling through both parts with the tap drill, is a perfectly usable order of operation. I do things a few different ways depending on the task at hand. Sometimes I have a part with clearance/counterbore holes already in it, then I'll use transfer punches to locate for the tapped hole. Sometimes I have a part with the tapped hole in it, and I'll use transfer screws instead. Sometimes I have both parts clamped together and do as you do and drill through both with tap drill, then open up for clearance. Sometimes I use the readout, and just go to the numbers. Most times I use the CNC now and just do it all with magic.
.
Having many different ways to accomplish a task with a few different tooling options is never a bad thing. There is no one perfect way of doing things for all jobs.