As far as I know, that's because way back when they introduced "new Reddit" (the redesigned web UI) they made the bizarre decision to use a slightly different a

As far as I know, that's because way back when they introduced "new Reddit" (the redesigned web UI) they made the bizarre decision to use a slightly different and incompatible Markdown parser. So ever since then, posts and comments have looked different depending on which version of the site you view them on. The URL escaping syntax is one difference, but another one is that the two renderers support different syntax for monospaced code blocks. As you can probably imagine, that wreaks havoc on the formatting of posts in programming subreddits.