Dumb question I'm sure, especially since I have 60 hours into the game, but do Skill points from Armor, do they count towards Perk levels?

For example, if I wear a chest piece that give +2 to Luck, and then I look at in the PIP boy I see +2 to luck skill, but if I look at the perk Tree, I see my non-adjusted Luck level of 4 stars, when I am expecting it to say 6. I also don't see any additional perk levels open up.

Am I wrong about how this works? Do bonus to skills not update the special abilities and their perk levels?

Now that I'm thinking about it, that probably doesn't make much sense, because it would open up a can of worms. For instance, If I picked a higher perk based on the armor bonus, and then changed armor, would I keep the perk level or would it gray out again?

Yeah, buffs from apparel or consumables won't open up new perks for you to use, only add to whatever that attribute increases. So bumping INT will give you a little more XP, STR carry weight, etc.

The perk page only considers your actual attribute when unlocking perks. The apparel (or chem) modified attributes are very useful in skill checks (graqe mentats are your friend) or in general gameplay. Swigging some moonshine, popping some psycho and then getting into a brawl can have interesting results.

no your clothing and armor do not affect what perks you can unlock just as they did not affect what perks you could unlock in New Vegas or Fallout 3 because you can take your armor off so they do not want you to add perks than switch your armor back to normal.