Would holes in the storyline engine count as secrets?

For instance, in Metroid Zero Mission, you can bomb jump your way through places you aren''t supposed to be in yet.

Yeah, i remember that. And in Metroid Prime you could sideways jump at the very beginning of the game to reach a platform which leads to an item you aren''t supposed get until halfway through the game. Then you can see how far you can get in the game having only a few advanced items but none of the basics :-)