I don't know all the anatomical details, but you can have more than one type of pronation, that occur under different circumstances.
A simple "wedge" which makes one part of the insole thicker than the other (such as I make for myself with tape) can balance your foot side-to-side.
But if you only have pronation during jump landings, which causes your knee to mis-align only when you land, or if the pronation gets worse during jump landings (and maybe take-offs), that can create long-term knee problems. (I have some of each type.) In principle, you can put tape under an insole on the inside of the foot, and compressible foam under the insole on the outside of the foot, to fix this.
BTW, the jump-landing pronation may be hard to evaluate yourself - it helps to have someone else (coaches are good) watch your knee while you land.
But you would need a fair bit of trial and error to get it just right. So you might experiment with modifying inexpensive insoles from the dollar store, rather than applying and ripping off tape and adhesive foam from the insoles that came with the boot. Besides, you may want a thinner insole so you have space to work with inside the boot. I've been meaning to play with this a little more myself.
That is something that your foot doctor can do too - he/she would might make a fancier looking custom insole out of fancy materials rather than using tape and adhesive foam. It's possible that a foot doctor would have the experience to do it faster than you can - at a price, especially if the doctor has to visit the rink to watch you skate.