For now I just build out one wing, control surfaces and all, and mirror it once it's finished - this seems to avoid the bulk of the problem, although it's possible my designs just don't suffer as much from it. One problem I haven't managed to tackle yet is control surfaces being modified when loaded as a subassembly - often one side is flipped and rotated 180 degrees.
Would just like to say I'm tremendously thankful this mod exists and is actively maintained, but I really really hope KSP2 has stock support for procedural parts, or is at least far easier to work with.