Frequent visitor, first time register, first time poster. So, I realize may opinion or view on this interesting discussion may not be equally relevant to the individual members of the community.
However, it's still a valid view and, as I find the discussion quite interesting, one I would like to share.
In my humble opinion, the question becomes 'What is 100%?'. That is different for each and every videogame and for some, very hard to tell indeed. However, for Super Metroid, it seems rather simple. The game tells you your item completion rate after a run. That is a very definite and hard measure by which to rule. And a very convenient one. As there is no room for interpretation or error.
So, in short... to this particular avid TAS viewer (me), what would make up a 100% run of Super Metroid? One that collects all items. If that involves somehow and for some reason glitching past entire sections of the game - I vote 'Yes'. For non-glitched, actual real time gameplay 100% completion videos, we have SDA and the like.