If you are looking at a spec that is lower priority than another spec, that checkbox says that you would respec a soulbind when using the spec.
Like, if you were necrolord and using Emeni for an affliction spec, which is your highest priority, with a malefic rapture conduit. When you look at your off-spec, say destruction, the optimizer will probably also want to use Emeni, but since you have an affliction conduit applied - it will instead opt for Plague Advisor with a destruction conduit. If you check the “allow conduit respec”, the optimizer will instead use Emeni for destruction with a destruction conduit, on the assumption that you will go back to the sanctum and change the conduit when you want to play destruction.