It can have other stuff in it.. you just have to open it and show them some fins or bcd etc. Then they give you an extra 23kg. We spread our gear around in our bags and they have never not given us the allowance. It can be a pain to have to open the bags so if you can, put your dive gear in the easiest bag to open in the airport check-in line or at least make sure it on top so it is easily seen.
@pinkpony not sure who you are diving with but unless you have a private guide you might not have a choice when diving with currents. Groups tend to be 4 to one guide so unless you are a group of 4 you will have other dive buddies. Hopefully you will be matched with divers with the same interest, if not you may have to miss a couple dives if you want to avoid currents altogether. High end boats try to accommodate everyone to the best of their abilities but lower end boats might be less inclined. This is not drift diving like you would experience in Cozumel. Most ops will try to get you in the water when it is optimal and safe.
I have always worn gloves and have seen people diving with knives strapped to their legs so I think it will depend on the operation. Raja is very warm compared to other Indo locations, but when you do consecutive dives your body temp does go down. I would skip the shorty and just bring the 3 mil. I just dive in skins with a hooded vest and will add a jacket if I start getting cold in Raja. There are a lot of little stingy things in the water so I would keep your legs covered.