penetration concerning mixed damage

If Ezreal builds mixed damage.. like say a new Korean build that has him as AD for first half of game and AP end-game. same build, Manamune > Iceborn Gauntlet > Seraph's but then instead of BoRK, get Gunblade and opt for Sorc boots switching to AP and AP scaling from Gathering Storm.

His Qs have AP scaling, but it does physical damage. Does magic penetration effect the damage he gets from its AP scaling?

What about the rest of his kit that's magic damage and has AD scaling? Does magic penetration work with the damage he gets from AD scaling instead?

I assume that's the way it works. Discounting on-hit effects, If the skill does "Physical Damage", then it does "Physical Damage" even if it has AP scaling. The AP scaling it has will count towards physical damage if the skill says it's doing physical damage.

So if he goes Armor Penetration, besides auto-attacks, the only skill that will work with it is Q due to being physical damage.

Seems like this is the reason why Koreans have been transitioning Ezreal into AP with sorc shoes and gunblade late game. The only physical damage he has in his kit is Q. Magical penetration seems to work with the AD scaling on the rest of his kit. Super cost-effective.