I do nearly the same thing, except, I drill the holes later in the process.
After sanding the front bolster area, right when you are ready to glue everything up, I epoxy on one side, then let it set. When the epoxy is done curring, I then use the holes in the tang as a guide to drill through the glued on slab. Then, I epoxy on the other slab, and let it cure. When it is done, I use the holes in the first slab as a guide to drill through the other side. I do this because I do not have a drill press. I tried your way once but without a drill press, the holes did not line up properly.
Anyways, that's how I do it. I use the same epoxy to, and everything else is pretty much identical.
Oh, and I just use the same size bit as the pin, but it is tight going in.
Firstly, I have no idea how you get good results without a drill press. So if that method works for you, then I say stick with it. (Drill presses are cheap, and will improve your results immensely.) I hope you're clamping the knife down really well though. Drilling seems rudimentary, but is actually quite dangerous.
But, now the problem with glueing a scale on, then drilling it is threefold.
First, you have a lot of time invested in the handle and if you have bad tearout, or bit wobble, or some other issue, thats a lot of lost time. I find out right away if the scales are trash due to drilling issues. If they are, then I've not wasted any time on them. I toss them and do another set.
Second, if you screw yours up, its glued on there. Now you've got a stickey mess to clean up before you can start over. AND also, you do
two glueups! Thats another bit of wasted time. You have to wait for the scale to set on there, drill, glue, wait, drill. For a one at a time hobby maker, that wasted time is OK. But for guys like John and I, we need to move on and keep busy when we're in the shop.
Thirdly. Drilling both scales at once, then finishing the bolster area with the scales pinned together insures that your scales line up
perfectly on each side of the knife. If you took your time finishing the bolster area (and actually used a hand tool or two), then they should be mirror images of one another and you should detect NO difference when holding the knife up and looking on them closely.