Markdown cards are intended as a quick and easy way to create content for your beacon notifications. You don't need to create different pages on your website, it's easy to edit and update and does not require any coding expertise. We will also launch more themes for markdown cards soon, which will make the cards much more customizable.
Custom URLs are more suitable when you already have a website with the content that you want to transmit. A website can be more flexible and can be used for complex things like taking user input and running custom code and scripts which the markdown card doesn't allow.