Daf Yomi - Sukkah 12 - Spiritual or Physical Clouds?

The Gemora cites an argument between Rabbi Akiva and Rabbi Elozar in the explanation of the possuk ki basukkos hoshavti es bnei yisroel. What are these sukkos that the Torah is Referring to? Rabbi Akiva learns that the possuk is referring to the booths that Hashem made for Klal Yisroel when they were traveling in the desert. Rabbi Elozar understands the possuk to mean the ananei hakovod, the spiritual clouds which surrounded Bnei Yisroel on their way out of Egypt.

It is evident from the Gemora and Rashi that these 'clouds' were regular clouds that are regarded as being produced from the ground and not susceptible to tumah. It would seem from Rabbeinu Bachye and the Targum Yonason on the possuk in Breishis that the ananei hakovod had the same physical characteristics as regular clouds, but there was an added spiritual effect from these clouds.

The Vilna Gaon in Parshas Bahaloscha learns like this as well. The possuk states that the cloud left from the tent and behold Miriam became afflicted with tzaraas. Aharon turned towards her and behold she had tzaraas. The Gaon explained that it was only after the cloud left that it was ruled that Miriam had tzaraas as the halacha is that a kohen cannot rule on tzaraas during a cloudy day.

The Ksav V'kabala in Parshas Shelach disagrees and states that these clouds were purely spiritual. The clouds could level mountains, raise valleys and kill snakes and scorpions but they did not function as regular clouds.

I saw in a sefer Imrei Chein that he bridges the gap between the two explanations, however I am not certain as to his precise explanation.