Thread:Rewet6/@comment-31463759-20170306214834/@comment-5956954-20170307225458

If I were to explain further with credit to What Hapen for pointing this out, Muffet's appearance and role in the story are almost exactly like Napstablook's battle before toriel and Mad Dummy before Undyne. They are both powerful mini-boss like enemies that are before the final boss of the area. The only difference with Muffet is she is more difficult and introduces a non-recurring SOUL mode. Even then, the game mechanics with the kill count do not lie, and Doggo along with a bunch of others like Pyrope, introduce new mechanics despite not even being a boss.

The other unique reason that she is not a boss (My own reason) is because she literally only serves to be one of the hitman hired by the real boss, Mettaton (I'll explain later if you don't get why), and has no other recurring role in the story outside of her lair. She's a bought-in character of course.