Dear Avira,
Your post is baffling. How is limud Torah not Limud HaTorah? Your trying to construct a system where one study is limud HaTorah and other study is not. Being that all the topics under discussion are using the same classical (Tanach, Mishna, Gemara, Etc.) Torah sources, how could it be different just because it’s officially being studied during Mussar Seder? To quote Rabbi Yochanon, Limud enables Activity.
It should be the same across the board. The level of study is only relevant to the level of understanding. Be it Mikrah, Mishna, Chassidus, the Kabbalah, or Birchas Shmuel. You would be better off learning Nefesh Hachaim correctly off-line, instead off using as a cover for on-line debate.