What does the verse mean when it writes that the Ark "was lifted above the earth"?
Rashi: It means that the Ark (eleven Amos of which were submerged) was clear of even the tallest mountain. 1
Rashi assumes that at the end of the Mabul, the water subsided uniformly, one Amah every four days, until after 60 days the mountain tops were exposed. Ramban disagrees, for at this rate, the land would not be dry for years! (There are mountains 10,000 Amos tall.) Moshav Zekenim (to 7:12) answers that below the mountain tops, the mountains decrease the space for water, so the water receded more quickly after clearing the mountaintops (also refer to 8:4:2:2). (To answer the question, he must say that mountains occupy more than 99% of the area above the land. Nowadays, mountains occupy a small fraction of the area! - PF)
Rashi writes: "The Ark was submerged 11 Amos into the water." Why does Rashi have to explain this here?
Gur Aryeh: The verse implies that the Ark was lifted off of the ground only towards the end of the 40 days of rain, and we might wonder why this was so. Rashi therefore explains that it was submerged deeply into the water.
רש"י: משוקעת היתה במים אחת עשרה אמה: למה רש"י כתב זאת?
גור אריה: לכאורה קשה למה התיבה התרוממה רק בסוף ה-40 יום? לכן פירש רש"י שהתיבה הייתה שקועה במים.