Yoma 30A - Meisech es raglav needs tevila

Gra Aleph brings that mesech es raglav needs tevila for R' Papa's reason. I always thought tevila was spiritual cleaning, not to remove tzoah. Is this a halachic tevilla with hilchos chatzitza? Also, perhaps a person can be spiritually clean, but still physically dirty and smelly.

Also Rashi on Mishna 28A tries to describe how someone who makes gedolim is hovering over his legs as he bends his knees. Even if I understood what Rashi was describing, I do not understand how that fits in with current metzius.

[By the way, it's ר"ב רנשברג, not the Gra]
I also was bothered by the idea of doing tevilah as a physical cleansing. But the gemara seems to be saying the same thing about קידוש ידים ורגלים - because of nitzotzos. And it even suggests doing it on only one hand!
Actually, the Torah itself always describes טבילה and קידוש this way: ירחץ בשרו במים, ירחצו את ידיהם ואת רגליהם, יכבס בדגיו... I'm guessing that the spiritual aspect is built around the real physical action of washing, and occasionally the gemara uses that equivalence?

Concerning the other issue about bending the knees etc., I'm not sure I understand. They didn't have toilets, so I guess that was the natural position to use.