I use TW’s wikitext for anything written natively in TW, and have no expectation to export from TW. This, to date, is the vast majority of the stuff I have.
Content that’s imported from another source - depends on the source. I’ve been importing various ad-hoc notes from other systems, where I’ve written them in something resembling markdown more than wikitext, so import them as markdown and cleanup from there. Otoh, some imports (from tomboy notes) I’ve written (still finishing) my own conversion tool, so I just wrote that to convert to each xml into a .tid directly.
Then there is content I expect to be exported in a raw form - notes and documentation I will send to others. This is in markdown, and doesn’t rely on any TW code.
In one TW, I have a longer term plan to use TW as a staging area for a static website, where the site will be written in markdown and converted using pandoc, jekyll, or other similar markdown->website tool, but my local storage will be within TW - acting as an instant preview. I’ve not delved into that side project much yet though, and I know TW itself can export individual tids to html too. Till I’ve had a chance to compare the various tools, I can’t say how that’ll go.
Also (more back on topic, kinda) it’s possible to embed markdown within wikitext, and pretty sure the reverse is possible too. But it’s not something I think is worth the effort most of the time. (the one place I sometimes switch formats internally is embedding a CSV to wikitext as a quick-and-dirty way of writing/importing a table - eg, like so:
$$$text/csv
height, tall
width, wide
length, deep
$$$
Final thought: does this sometimes mean I write formatting in wikitext/markdown when the other is needed? Absolutely (and 99% of that is sublists). But it’s easy to spot and fix so doesn’t bother me overall.
It does occurs to me writing this, that a css class set for the different content types would be neat, meaning I could (in edit mode) get an immediate visual hint to which type it is). But that’s a minor polish on the overall workflow.