I'd recommend countersinking all your holes for three reasons:
1) it reduces possible strain points during heat-treat
2) it makes pin insertion easier both during fitting and when everything's covered in epoxy
3) it leaves a little space for epoxy to pool and grab your pins some more.
I used to use a larger drill bit. This works, but is lousy if you want to leave a hole exposed for some reason. The bits chatter, standard bits are long and have runout, you get eccentric chamfers, etc. A proper countersink bit is inexpensive and is the right tool for the job. I prefer the single-flute bits OR the conical ones with the sharp hole-through cutting edge. Don't know how else to describe them. Those are THE BEST, IMO, and it makes a difference. At home I have only the multi-flute and the single.
-Daizee