Sounds like you got good news, and now you know for sure :thup
Since you have extra holes, you may be able to use them to your advantage. Here's why I say that: A "blind" hole is always hard to fill, because air gets trapped in it. So when I can, I make a blind hole not be a blind hole. SO much easier to fill (especially if it is relatively narrow, and hard to get to the bottom).
1) Connect some adjacent holes (such as, when I did my bow pulpit holes, I connected all three with some small "tunnels" in the core - was not hard since I was overdrilling anyway.
2) If necessary, drill a purposeful "relief hole." This isn't needed often, but for example, when I did the holes for my trim tab upper attachments (on the vertical transom), I ended up with an "upper cave" above the hole (from overdrilling). What I did was drill a very small hole on the inside of the transom (this was behind the fuel tanks) at the apex of the "cave." Made it easy to fill from the bottom/outside until a bit of thickened epoxy started coming out the upper hole (like doing an outboard lower unit).
3) Or, sometimes you can use a syringe and start at the bottom of the hole and work up (can be tough on relatively deep narrow holes).
So anyway, perhaps you can use those holes to make some air relief tunnels.
What I do when I'm filling is put blue tape over the whole shebang on deck. Then I use an X-acto knife to cut the circles out of the tape that are the holes. Sounds fussy, but for me beats going around with a million little bits of tape on the edge. Then when I fill I just let it slightly "muffin top" over the hole, and when it's in the green stage (rubbery but not sticky), I slice off the muffin top with a chisel, and voila, flat deck again. (Then re-drill later.)
Sometimes I fill from below - just depends on air situation. If you "paint" the inside of the holes with neat (plain) epoxy first, then fill with thickened epoxy, it works out better.
Glad you did not find a worst case scenario (even though even that could be fixed).
BTW, I don't think a "pin" type meter works very well. I'm not sure why, but I just know those aren't used (but maybe they do work if you can touch the wood inside?). Typically it's surface meters that are used. 'course you have seen the real thing now.