Is there a way to change the thick blue blockquote color in markdown EDIT mode. I know it is possible to do it in the preview window with CSS, but I can’t figure out how to change it in the edit mode. I find it quite distracting and would love a cleaner look. I thinner line in a grey color or indentation.
You can’t. The visual appearance of edit mode is determined by DT internally. Probably trying to be close to the default CSS used by DT. And if I recall correctly, bookmark styling was advocated for in the forum 
If you really need an MD editor with configurable visual styles, you should use an external one.
I’m enjoying the internal markdown editor, and it has many advantages over using an external editor. My hope is that Devonthink will keep on improving the customisation of it.