It looks like you’re over-extruding right now - which may very well be contributing to the problem. For example, if you’re actually extruding 110%, that means you have an excess of 10% of the plastic that needs to go somewhere, and filling in your holes is a great place for that extra plastic to go!
There are two factors that go into the extrusion - diameter of the filament, and the length of filament that’s pushed through for each step of the extruder motor. The first is easy – use your calipers to measure the diameter of the filament you’re using (every reel is different, and sometimes for lesser-quality reels, it’s different at different points in the spool!). Measure it in several places in the first meter or two of the spool, and average those readings. That gets entered into your slicer. In my experience, the 3.0mm filament is supposed to be 2.85mm, but most of mine tend to be in the range from 2.88 up to 2.95 mm. Check that often, and make sure you update that figure in the slicer whenever it changes (and whenever you change the spool of filament, of course).
The other factor is how much filament gets pushed through for each step of the motor on the extruder – that’s the e-steps value, and is unique for each tool-head (at least for the classic tool heads, I think the aerostruders are less variable, but don’t have any of those heads). The value may be on a sticker on the back of your tool head, but I prefer to measure using my filament and set it myself. Here’s a guide to doing this: https://ohai.lulzbot.com/project/fine-tune-mini-extruder/calibration
I’ve update my e-steps often; going through the process is easy, and it forces one to pay close attention to the mechanics of the tool-head, which has been helpful in spotting early signs of trouble twice now for me (cracks in the idler assembly, for instance).
The e-steps doesn’t change very often, so you set that in your printer firmware (per the link above), not usually in the slicer. The filament diameter is very often changing, so that gets set in the slicer. When correct, you should find that a 1mm hole may not be 1mm in diameter, but it will certainly be open rather than filled up with plastic.
One final thought – you might be printing slightly too hot – if the plastic is too hot when extruding, it can flow too much and fill in the detail. On the other hand, when its hot like that, it tends to adhere to the adjacent layers better, so the part is stronger. It’s a tradeoff.