Edited to say: I was indeed missing the obvious, please ignore this post (if you prefer I can delete it). I was getting confused as to who did what. The inconsistency is not in the plugin. Joplin is handling the whole markdown="1" thing even on the editor side.
Original content
Hi, I'm just trying this out for the first time. Looks good! But (you knew that was coming, didn't you 
) ...
It appears to require the HTML attribute markdown="1" to be set before working inside embedded HTML blocks like div. I have two issues with this. First is that I have lots of notes written when I didn't know such an attribute was being introduced by various tools, and second it is inconsistent with how the Joplin preview works. See the attached screen capture.
The preview is always applying markdown against embedded HTML, while Rich Markdown requires markdown="1".
Ideally I'd like there to be a default in the options (to be used when the markdown= attribute is not specified). Possibly it should be in the Joplin App options to control how the preview details with it, and then maybe a separate option for this plugin? And then if the source provides an explicit markdown= attribute then that can override the default. That way we get to manage this according to our own history and preferences.
Please forgive me if I've missed something obvious. I looked for existing settings and didn't see one for this. Tried on both v2.12.8 and v2.13.6.