From the next build on, we've added
$ (dollar sign),
] (square brackets), and
* (asterisk) to the whitelisted characters that we allow to appear unencoded in links. It's debatable whether that's necessary or legal or unnecessary or illegal by the standard, because the RFC situation is horribly confusing in this regard. In particular the square brackets are a strange beast.
However, since there are advantages like certain sites simply not accepting encoded asterisks (your archive.org is one example; Google is another one), and plain readability of links, and since whatever is necessary to make sure URLs are transported over the network correctly is done by the browsers anyway, I consider this a good change. A major reason for encoding those characters was the potential of collsion with characters that have special meaning in Markdown, but that problem can be solved in another way.
Note that there is no change to free-form link recognition (a.k.a. "this looks like a URL, let's link it").
But if you explicitly make it a link (with angle brackets, or
[...](...) syntax, or Ctrl-L, etc.), these characters will not be automatically percent-encoded anymore (again, next build).