I do tend to build Protobelt in between Lich Bane and Deathcap, though I don't consider it a core item since it isn't essential to deal damage; it isn't like Lich Bane that adds a significant damage on Phase Dive or Deathcap which increases Ekko's damage by an effective 30%.
I have noted in the build that it is possible to delay getting the core items in favor of another item in certain situations.
As for the runes, I have never used Hybrid Pen, so I can't make a judgement on their effectiveness, though I can see the appeal.