The markdown has to be at the lefthand margin.
Because of Tailwind there is no style and styling with markdown is cumbersome. Do you have to use Tailwind in these pages? No, of course not, you could write a markdown friendly stylesheet.
What would you do with shortcodes? In many ways, shortcodes show the limitations of markdown for any content that is more than just a bit of text. You'd have to write a shortcode like system in PHP.
BUT! I've just seen the Laravel Mail integration and that uses Markdown formatting for emails AND the templates use Blade components. Your shortcode system is already there, in Blade.
Alternatively, keep markdown for very basic styling (Rich Text anyone?) that represented content as paragraphs of markdown that build a page. It would be like back to Fronter or the original Rooster. Then you are just recreating what you could probably do in Wordpress.