So far, I can confirm what you describe. This is actually an improvement from 3.4.5, which I was on before your report, where neither this plugin nor my click-to-copy plugin worked at all. Now both work after the note reloading you described.
It seems like this is all related to the recent addition of the mobile Rich Text Editor somehow - there are a couple of bug fixes in 3.4.6 that reference this plugin directly, even.
I don’t know if the fault with the remaining issue lies with my plugin or the Joplin updates, but I will do a deeper dive soon to figure out if it’s something I can fix on my end.