Things at the right of the endpoint should not play unless you purposely place the playback arrow past the endpoint.
Edit : Regarding export of the song to other formats, I am not sure how they work but I presume NSF and famitracker do not have such a end loop point, only a song end. Then I think the special endpoint, which would be a special famitstudio feature, should be ignored so that the material in the reserve is not lost in the conversion.