For Item #3, I have asked for that in the past as well..

Still feel we miss a application.css per theme is required. not just a global single one, exactly for these scenarios, and colors as well .

DAW, any plan to support additional custom css file per theme ?

Something like,
.\AppHtml\CssThemes\<ThemeName>\theme_custom.css or application.css under the theme dir ... but using the same name could cause some unnecessary confusion with the global application.css file.