IIRC multi-stage missions can sometimes have surface restrictions for one part and underwater ones for the other (biolab, for example).
I don't think OXCE engine provides a possibility for different item restrictions for multi-stage missions. Looking at the changelog, multistage support was added way back in 2018, but itemcategories are not supported (see the example ruleset in
https://openxcom.org/forum/index.php?topic=4444.msg91852#msg91852). I'm not sure what that would even mean technically mean (would you essentially only be able to use dual-use items, because you can't bring underwater-only items to stage 1?).
I'm 99 % sure I've used surface-only stun grenades in biolab level 2 ("underwater") and was unable to bring DPLs there.
Now checking the ruleset, part 1 has starting conditions STR_SURFACE, and the second part suggests that the underwater starting conditions don't actually apply (at least to items):
startingCondition: STR_UNDERWATER
(...)
depth: [0, 0] #Because startingconditions dont work.