Tib said:
Question: do the passive bonuses get increased with +skills from items/charms? Or is it like synergies where only actual points affect the end result?
Depends on what you are asking

The skill levels increase, and therefore all the bonuses increase as displayed: critical strike, AR% from penetrate, piercing, D/A/E, Valkyrie level --- all goes up.
It is, however, possible (I don't know) that the "valkyrie gets bonuses from ..." don't apply for levels gained via items --- depends on whether these are actual synergies, or just displayed in a similar way.