Quick answer: A solid piece of advice the Brits (BHI) imparted to me in their courses, which is promoted in all respectful traditions, is to ALWAYS make any new material fit the original work, and never the other way round. I do this even if the work has itself may have been altered. Battle scars are part of each clock's war stories...so, I would not drill, either. Just trim the finials.
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There's a lot I've learned here from the gang. Way more to come, I'm sure. But, it's essentially experience and detective / forensic work.
On many of these, the top board was not actually the crown, see photos of some reconstructions. Not sure what the various part names are, but if you look carefully at your top end you may (or may not) see faint dirt or finish lines from where another piece of wood may once have been mounted perpendicularly on the top, like in these photos. Often they were installed via a crescent shaped slot-cut maybe 3mm wide and 15mm deep in the center cut with a "quick dip" of a circular saw. I think it's called a "dai doh" or something like that where the blade intentionally wobbles, as shown by Norm Abram. Maybe the makers chose finials for some cases, crowns for others or both --so the holes in your clock (the top) may have never been used? We may never know. Choose the look you like, in keeping with what you think once was?
Anyway, I don't think different sized holes would be enough to say whether any part is original or not. Your finials look good and I hope they match the existing wood(s) and the other finials if any survived. I'm sure they will all look good when you're done. Match the finial you like best for each individual hole, then trim?
I would probably just scrape with a paring knife. It's not a balance staff. And I would make a slight taper and any other shaping needed to make them sit right and sit tight. Make a few test fits and only whack them home when gluing. You might want to take an old threaded bolt, smaller than the diameter of the holes and scrape out as much old glue, dirt, wax, etc. as you can before you start trimming. If you do overshoot, as you likely know, a few drops of water will expand wood like a sponge and much of it will stay after the water evaporates. We do this because it's fun, so there's no reason to hurry ;-)
All the best!