Update: I think there is something that is not being updated properly on the led map when the keyboardio gets started.
I was able to use FuncionalColors (FunctionalColor v3 - Dynamically Label Active Keys with Colors), which is my favorite led plugin, and there is an interesting development now: when FunctionalColors is running, the keys that did not have leds on are now lit with the expected led colors. Even the brightness behave properly. When I switch to the function layer, the colors are correct. When I switch to the numeric layer, the keys that are redefined on that layer switch off.
I found out that removing NumPad from my sketch fixes my problems.