This seems a little odd to me, so mine expects the actual HMTL link [Visit page 2](page2.html). However, that breaks compatibility with GitHub pages and will probably annoy people. I'm thinking the better behavior would be to for [Visit page 2](page2.md) to look for the .md file at site generation time and if it doesn't exist, generate a link to an .HTML file instead.
Mind is a little fuzzy lately so I'd like feedback on this idea.