How should I run stripped cable through conduits?
There are (at least) two problems with this, and the solution to both is to change to THWN (or another wet-rated labeled conductor) when you change to conduit.

Problem one is that stripped NM is not labeled and not acceptable per code for that reason, as @Speedy Petey said.

The second is that you are running to an external location, which means that the conduit is by code defined to be a wet environment, and even with the sheath on, NM is not rated for wet locations, but you need a wire that is rated for wet locations.