I just ran into this myself and had a bug report rejected since this feature request already existed.
I’m not sure I agree with treating this as a feature request; not supporting reference-style links with URLs that work in other contexts should be treated as a bug as Obsidian is not correctly handling Markdown (for reference, see Basic Syntax | Markdown Guide).
I agree. This lack of support for standard markdown is the only thing preventing me from switching to Obsidian, as it doesn’t work with my existing notes. Nor would I even want to migrate them given the absence of this feature, since the whole point of that link style is that you don’t have to put long links in the middle of the text, possibly many times. It’s unfortunately a deal breaker for me, which is a real shame.
Obsidian claims to support markdown, but it doesn’t actually work. Clearly a bug.