I just bought Metroid : Other M for $13 Brand New

"It could theoretically" -- Saying something like this means you had to invent a reason why an irrationality happened. In a well-told story, you shouldn't have to. His already poor reasoning makes even less sense when he tells her to use those things later in the game. I guess the wildlife or potential people/soldiers in the neighboring rooms suddenly stop mattering to him at a specific point in the game. On this point, the writer either was being outright lazy, or is a very bad writer.

Well, it shouldn't all have to be spelled out. Some of it is pretty straight forward logic. The main point is that some of the equipment has the ability to put not only Samus but the entire crew at risk and that it had to be checked out first if the equipment is safe to use. That's the argument they use in the game. Take that and decipher it how you please.