Jeff
The only answer is, "It's your plane. Build it the way you want."
That sounds harsh but every builder makes those decisions.
Some go totally "Comando".
Others Alodine and spray Akzo.
Find what works for you and go for it.
Personally I think both mating surfaces should have protection.
FYI
I sprayed everything with P60G2.
My process is debur, scotchbrite with maroon, dimple, wash with grey scotchbrite and Bon Ami cleanser, dry and prime. Not necessarily on the same day but the window between cleaning and priming is never more than one hour. Aluminum Oxide reforms within two hours of removal. Paint won't stick to it.
My $.02, YMMV