Of all the issues, this one is not the fault of Tiddlywiki. It is not even an issue to be honest, mere inconvenience. When Tiddlywiki started out, markdown was also in its infancy. However later years saw markdown emerge as the markup of choice among note taking applications and static site generators, while Tiddlywiki refused to follow the trend for the sake of backward compatibility.
Tiddlywiki did finally decide to support markdown in later years. However it is still afforded a secondary status. For eg; if you take a note in markdown, your metadata for the note is stored separately, as opposed to the front-matter like system used by Tiddlywiki markup.
If I write a note in markdown, I have the option to open that same note in no less than 10 different note taking applications and continue without missing a beat. In contrast, I cannot think of a single alternative note taking application that supports Tiddlywiki markup. Of course you can export it to HTML and convert it from there to markdown. However as we all know there is no perfect automation when it comes to unstructured data like personal notes, and you will end up having to confirm parity manually.