Your workflow is different from the usual workflow in KiCad, and that can be the reason of your holes looking differently. Maybe they’re covered by solder paste, or any of a dozen other things.
I often have a different way of operating, (which drives other people, especially “teachers” crazy sometimes).
I tend to “fool around”, experiment with features. “What is this?”, “How does that function work?”, “What are the caveats when I do it this or that way?”.
I can spend quite a lot of time on that, without making any visible progress. And then, when I’ve gotten familiar with a decent sub-set of the functions I can do a conversion relatively quickly.
Another way is to do it step for step, “One problem at a time!”, and this looks like steady progress. But you may well spend a lot of time of getting one of the intermediate steps right, and then discovering three steps later that you should not even have done that earlier step at all.
Therefore I recommend to fist get to know KiCad and how it works. Use your existing project, but just punch in some holes at random locations, and verify all the way to the Gerber files that these holes are defined as they should be.
For such tests you just need a few polygons and a handful of holes, which do not even need accurate placement. If you skip the “neat” steps, and the repetitive operations of getting 100 holes right, you can do a lot of experiments in a short time frame.
---- 8<------- 8<------- 8<------- 8<------- 8<—
And now the only remaining question is:
What does a handful of holes look like?