To answer most of these questions:

I organize and read everything in Zotero (with the night mode plug in), and make highlights for quotes, very brief annotations, or add #lu (look-up) for citations I want to search up in bulk later. Then I use the Zotero Integration plugin to pull the quotes, with citations and annotations into obsidian (into a note with a standardized title like: lastnameTitleYEAR).

I've gone back and forth between using Zotero to "Create Note from Annotations" and then importing that, versus importing it directly from the Zotero pdf. I've been using the latter though because it comes with hyperlinks that bring me directly to the location of the highlight in zotero from obsidian. But I think you can create a custom template for the first solution that gives you the same thing. I still do the "create note from annotation" even if I don't import it because I have a custom search that shows me every pdf with a note attached, which means I've read and annotated.

I also write out some notes digitally with a pen on my laptop in onenote (I kind of hate it, but it works) and then insert that pdf into the Obsidian note. But if I ever need that in plain text, I have to retype it because my handwriting is shit and the recognition software needs too much babysitting. Retyping can be helpful though.

I wish zotero's pdf reader supported pen annotations and clipped them into images on export, but unfortunately it doesn't. Xodo works well with a pen, but fuck if you can export that easily, and I'd rather not comb through pdfs to find notes.

I fucking hate word. I've been considering learning LaTeX, but I just don't need like 99% of its functionality, especially not now, and markdown is easy and useful enough. I like how obsidian lets me see my notes in folders, and then opening them in tabs quickly. Way easier than managing a bunch of word docs. Its search functionality is also great. There is a ton you can do with obsidian in terms of hyperlinking to other notes, or specific sections of them. Like, lets say you have a note of annotations, and you have added a heading (#) to a certain section, you can type [[notename#heading]] and it will link directly to that part of the note. You can also pull that section from one note to be displayed in another using ![[notename#heading]] and it remains editable. All of this will autofill too, so you can do "![[no" and notename will come up, hit tab, #, and it will show you the headings you can use. Take a peek at the documentation to see if it would be useful to you: https://help.obsidian.md/Home. Like you can even use CSS and embed iframes for whatever reason lol

While it is markdown, it is also partially WYSIWYG as it will display the formatting right away. So it looks quite nice while working. You can definitely export markdown to word (or anything else) when needed. But obsidian may be an unnecessary step for you? I'd play around with it and see if it is useful though. There are a few good videos out there, but jesus christ, most people seem to be using it to pull shitty self-help articles as though that is in any way useful.

Unfortunately, when I needed this workflow the most, I did not have it. I just did everything in word. Currently, my primary use case for this workflow is personal research, so most just stays in Obsidian. I usually just export right to pdf when I need to for work, or I just reference in obsidian for speaking/taking notes.

I use obsidian for everything now though, it is my primary note app for anything I need, from pulling annotations to shopping lists. Its one of the best designed and most useful pieces of software I have ever used, and I barely even go past the surface features.

Do you use Zotero? It does such a great job at managing metadata for how janky it is under the hood. The firefox plugin lets me grab papers and metadata very easily, and categorize them on the spot. It will also redirect to a library proxy which is nice. It has basic RSS for seeing what journals have published recently and you can add it to your library directly from Zotero (can't remember if it will use the proxy or if that only works with open access.) Also, being able to search the contents of all the pdfs is honestly amazing. I think windows search allows it, but is way less efficient. I use the zotfile plugin to use a cloud service to sync everything between devices too, instead of paying them for that.

edit: wow, you can hold control and hover over a note or link in obsidian and it will preview it in a pop up. Can't believe I didn't know that lol