You aren't really supposed to use the nvse_loader.exe at all to load NV with NVSE. It's used for the GECK editor, but not the game.
Steam's in-game overlay loads NVSE.
Your batch file should have "FalloutNV.exe" as the second line to bypass the launcher. Unfortunately it still doesn't load NVSE and I never found a way to bypass the launcher and use NVSE at the same time.