In my Wingship II I can't use the built-in items because I don't have enough equipment skill. In C1 you didn't need equipment skill for built-in stuff (like the T20 cloak on my Sniper's juju). So, I don't know if this is a bug or a feature In my opinion, the 50 SP I needed JUST to get piloting 4 should be way more than enough to use all of the features of the ship.

I think it's intended to be so, I can use my juju's cloak aswell in C1 but I can't use the app ward's SSS on my alt due to lack of equip20 on it

It's a question of using versus activating the in-built gear. Even in C1 you can't use inbuilt gear that you don't have the skill for, but activating a cloak that's already equipped is fine.