Can I apply a finish safely over top of these wax patches?
Given their size (10mm diameter is a pretty big wax fill for finish to bridge over) and that it seems there are quite a few I think there's a good chance that you might run into a problem down the line, even with the very hard composition of most wax sticks.
However that's just my thinking and you have something that already gives a result you're happy with visually, and you're already set on doing some tests before going ahead, so let's start with that.
Using what you have
After doing the fills I think your idea to use shellac first prior to the poly is very good, given shellac's justified reputation for being an excellent intermediate between dissimilar materials and that it's rather famed for sticking to nearly anything.
- make sure the wax surface isn't too smooth (which is all too easy to achieve if you finish off cleanup up the wax by buffing the surface with cloth, which is fairly commonly recommended). Much better to leave the wax surface with some texture to give the shellac as much to cling to as possible, so when fully flushed do one final sanding using whatever your chosen finishing grit is.
- IF you have the option, use a shellac that is neither dewaxed nor bleached. The more highly processed shellac is the further it is removed from its original much-vaunted qualities1.
It's usually a better idea with any sizeable void in wood to fill with wood when possible, and since these are drilled holes of course you can easily make face-grain patches by using a plug cutter2. However even at the best of times plugs often don't give a completely invisible result and with highly figured grain by some of the holes you'd need to do some careful touch-up work3 to even get close.
An alternative worth considering is deliberately going for contrasting plugs and not trying to hide them at all. Going one stage further you could forget that you have neat holes and go for Dutchmen patches for some (or all, with varied shapes if you like). These are honest repairs to material with surface defects and they have a long history, so in many ways they are the woodworker solution.
One final thing you might want to consider is using epoxy mixtures in place of the wax. There's no reason you can't get a result at least as good as with the wax sticks using coloured epoxy and the repairs will be much stronger, plus the material is known to be more finish-friendly.
1 And if it's a concern, oil-based varnishes have absolutely no difficulty in sticking well to shellacs that haven't been dewaxed.
2 A tapered-plug cutter is best since these ensure the tightest fit (minimising the chances of a visible glue-line ring).
3 After cutting the plugs from plain/featureless wood it's then ossible to mimic both the grain (by scoring/cutting) and colouration (using oil paints, coloured shellac, tinted finishes, even coloured pencils). But it's not easy to get an invisible result this way, even with prior experience, and missing the mark can make the attempted repair look amateurish which are two reasons why I would personally favour not going this route.