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Have you tried to open a joplin .MD file in a plain text editor? That is not markdown. Its markdown wrapped into some Joplin format.
Can it really be migrated 1:1 to another app?
I can't say whether it can be cleanly migrated to another app but there are a number of export options to get you either to plain Markdown or something else within reason. When using the export option, the resulting Markdown at lest gives relative paths to any included media.
I don't think it's fair to suggest it's not using Markdown. It just has a wrapper around it to make it work better for the usual use case of being a digital workbook.
Joplin's notes can easily be exported as standard markdown (File | Export All | Markdown).
When I was evaluating Joplin and Obsidian for my notes, I switched between them multiple times and it was very easy. The folder of markdown files exported from joplin can be opened directly as an obsidian vault. The only issue is if you had resized any images with Joplin's rich text editor (doing that converts the images to html img src tags, but that was easily fixed with a script to convert them back to markdown links)