A bug in the way the application deals with plugins or with the plugin itself?
e: Looks like the reason for why https: links doesn't work is because : is converted to UTF-8/Windows-1252 %3A in the HTML DOM. While %3A is Ascii encoded for :, it does not actually work in the href="" value without actually being a :. I don't know if this is because of something Joplin does, or if it is something else though.
e^2: Didn't work in Firefox Developer Edition.
e^3: Well, hardcoding "https://" into the return value does work, it's far from ideal, but there's still the problem of the rendered output not being included in an export.
return '<link href="' + escape(token.content.trim()) + '" media="all" rel="stylesheet"/>';
Hardcoded version:
return `<link rel="stylesheet" href="https://${escape(token.content.trim())}" media="all"/>`;
e^4: Looking at how the href value is treated, it seems to be the path that is the problem.
/Users/user/Downloads/JoplinProfile/test.css is treated as file:///Users/user/Downloads/JoplinProfile/test.css
Meanwhile, C:/Users/user/Downloads/JoplinProfile/test.css is treated as file:///C:/Users/user/AppData/Local/Temp/1l3Gmwf908YIor5JaIooxNZsQcC/resources/app.asar/gui/note-viewer/C:/Users/user/Downloads/JoplinProfile/test.css
So while linking a local .css still doesn't work for some reason, it at least explains why one gets a default square while the other one doesn't.
e^5: Doesn't work in a regular v1.4.19 install either, so at least not an issue singular to the portable version.