> 1. Seems unavoidable because there is no natural order for these two elements.

There is a solution: restructure it so the href part is inside the link, rather than adjacent to, which is the real problem. reStructuredText had `text <href>`_. In that form, the trailing underscore is a wart, but there’s more justification to it than it may initially seem (where Markdown can have [text] or [text][], reStructuredText’s equivalent is text_ or `text`_). For my own lightweight markup language, I’ve been using [text <href>] for a couple of years (and had {text <href>} before that).

> Parentheses in urls often end up percent encoded whether they need to be or not.

That’s what you can expect from something implementing RFC 3986; but these days, almost everything uses WHATWG’s URL Standard <https://url.spec.whatwg.org/>, under whose rules parentheses are not percent-encoded.

> I actually don’t think that matches the way people usually write urls in non-markup formatting

It isn’t any more, but it used to be very common.