Really awesome writeup 
I found that it was slightly confusing for me in regards to the templates, so I think the usual workflow is to extract annotations from the pdf using zotfile, then go to the main zotero item (not the extracted Zotero note item but the parent) then do full export of the note in order to get the metadata to work.
For my Mdnotes Default Template.md file I use:
---
aliases:
- {{title}}
- {{citekey}}
---
type:: #Source #Paper
authors:: {{author}}
source:: {{pdfAttachments}}
year:: {{year}}
## Abstract
{{abstractNote}}
## Summary
## Notes
{{notes}}
so I usually fill in the summary when I import the note into obsidian, hence it is just an empty field here.
For my Zotero Note Template.md I just have:
{{noteContent}}
In terms of annotations, for me:
- yellow is the key contribution of the work / findings / key argument
- cyan is talking about the field of the problem or approach
- magenta is experimental stuff i might want to look into doing too
- green is to follow up literature
I followed OP for the rest, so my colorCategories in Zotero are:
{"Black": "", "White": "", "Gray": "[[Argument]]:", "Red": "[[Disagreement]]:", "Orange": "[[Critique]]", "Yellow": "", "Green": "- [ ] #litreview", "Cyan": "[[Field]]", "Blue": "[[Confusion]]:", "Magenta": "[[Useful for Research]]:"}
I have had issues with the exported note having escaped characters like
\[\[Field\]\] and \- \[ \] although I have disabled HTML conversion in obsidian and am using mdnotes 0.2.0-alpha4. Is there a setting I am missing?
