Pandoc solves most of the shortcomings of markdown. I've written papers and Thesis with it. The main problem is that it isn't standard and some missing features

Pandoc solves most of the shortcomings of markdown. I've written papers and Thesis with it. The main problem is that it isn't standard and some missing features need additional plugins. So your pandoc-flavourved markdown doesn't properly render in GitLab/GitHub.