As you all know you are not wearing armor when in the Vampire Lord form. And, the mage armor perk in the alteration tree will improve flesh spells.
I just want to know: If I am wearing heavy armor, then I cast a flesh spell, and, then I turn into a Vampire Lord. Will the mage armor perk be active since I am casting the spell wearing armor even though, afterward, I am not?
21 Answer
Yes you do.
This is pretty easy to confirm. You can use the console command player.getav damageresist to see your armor rating without having access to the inventory page:
My vampire lord's armor rating was 325 before casting stoneflesh (which is supposed to be a 60 point armor boost), and after casting it it is now 505 (which is a gain of 180 due to mage armor x3 effect). My normal armor rating went from 492-552 so I didn't gain any perk effects while not in vampire lord form.
Now, considering the spell effect will wears off after a short time, its not too useful for the 3 perk points you must spend, but if you have a mod such as Invested Magic it becomes much more useful.