What's the right way to do skinned mesh replacement at runtime?

What I am trying to do is to replace a skinned mesh with another that comes from different fbx file, and they share the same rig.

It seems there's 2 options,

Either I just copy bone transform references from old skin to new one, that means these two meshes should depend on exactly same bone list with exactly same order;

or I can find all bones in character hierarchy one by one with bone names for new skin, but that means lots of performance lost because I have to leave the "Optimize Game Object" option unchecked.

Do I misunderstand anything here? Any chance somehow I can get bone transforms with "Optimize Game Object" checked? I'm sure bone transforms are still there, just need a way to get them.

any comment will be really appreciated :)