Note: below post is offtopic to the discussion of the original bug.
So you’ve found a trick to make references render as if they were proper references. Nice!
No offence intended, but why waste time collecting all those links in APA/MLA format and not stick to plain https:// reference, if you’re not publishing in academic-like format? On the one hand, that is really time- and energy-consuming and makes your system less sustainable, imho. On the other hand, should you ever need academic-style references for a specific piece of text that you intend to publish, it would not take much time for you to gather all the mentioned sources into Zotero (or even Obsidian) to perform proper reference arrangement.
For e-books, if I understood correctly, you’re reading and copying & pasting simultaneously. It makes sense to separate your reading and note-taking process from your thinking process and definitely from your copying & pasting process, see e.g. here: https://twitter.com/fortelabs/status/1131963693821026305
Again, sorry for the unsolicited advice, I only make them because I’ve been struggling with similar workflow issues myself and wish someone could point me to a convenient procedure, you can definitely ignore them if you’re fine with how you work.