If you want to have something represented exactly, you should use backticks around it to specify that. I’ve edited your original post to make it more clear.
Also, according to the original Markdown specification for links, the parens must “immediately” follow the closing square bracket:
To create an inline link, use a set of regular parentheses immediately after the link text’s closing square bracket.
So it would seem that whitespace is not allowed, at least according to the description of the specification. Additionally, the CommonMark specification, which is a much more rigorous specification of Markdown, does not allow whitespace between the two parts of an inline link.
If GitHub.com accepts whitespace there, it is a bug, not something that should be replicated in Atom.