A main goal of Markdown is to be easy for anyone to use. Having to substitute characters in a URL string might be fairly trivial for you or me, but certainly not for everybody.
On the plus side, having a simpler syntax for URLs I feel is more readable which is great for ease of use. I think ~ looks like a link, and @ makes sense semantically.
But to be sure I think the legacy syntax could remain as a fallback / alternative. New syntax is something that could be tried in a flavor.