Couple’o things:
Consider the possible answers here: 18.04 - My laptop battery never charges to 100% and it stays on 99 - Ask Ubuntu (yes the answers are a pain in the ass but I’ve yet to see a guide that points out how to force the recalibration with a live system)
And have you tested charging from all possible ports when at 99% and seen if any one of them pushes you up to 100%?
You mentioned here: Laptop loses charge despite being plugged into stock USB-PD adapter while powered on - #5 by nomb85
… that the charge percentage is inconsistent across plugging in and unplugging cycles. The next time you plug in, check the Watt-hours reported on the battery (energy, energy-full, and energy-full-design). Then the next time you go from seeing a shiny 100% to a 99%, do it again. Then when you go back to 100%, do it again. Record everything.
If the energy-full is going down, that’s degradation being caught up to by the OS (I think). If the energy is dancing around and energy-full is staying still, then something weird is going on. If energy-full is dancing around, then something really weird is going on.
Disclaimer: not an expert just guessing.