Ye may be mixin' yer metaphors (so to speak). You won't find too many mountains that are 5,000' top-to-bottom, but would you call a 700' hill rising out of a 6,500' MSL plain a mountain?
Certainly MSL altitude factors into what we know as "mountain flying", but I've flown over a 2000' vertical rise mountain at 2600' MSL, and I've flown 500' AGL over table-flat terrain with 6100' on the altimeter.