Oh yea also something else.. You said in the dagger+sword section that they don't mess with each other, sorry to say but they do.
If you have sword on your main hand (as you will have) the main hands weapons skill will be calculated 1st. Meaning at fixed, the calculation would go:
Melee hit -> Calculate skill activation (73%) if "yes" Phoenix hits if "No" then calculate 2nd hand weapon skill (15%) if "yes" Penetration hits if "no" then calculate normal melee formula (agi, rates and stuff I CBA to explain here).
So yes, Phoenix WILL mess with Penetrations activation due to higher activate rate. In an episode where it would allways miss, it wouldn't since it wouldn't hit letting Penetration to have a chance to hit. So as long as Phoenix is there, it will block Penetration to even have a chance of activation due to Phoenix activating. Meaning that Penetration has only 27% chance to even go trough the calculation of does it activate or not. Hope it doesn't sound complicated, I'm bad at explaining stuff except if I'm in trouble.