If you are sensitive to these issues, unfortunately you need to go with a mainstream linux distribution and use near-default settings.

It's great that you can customize everything and use your own window manager, compositor, etc ... but these issues are the price you pay. It is unfair to compare this to Windows, where you don't even have these customization options.

Specifically for the network manager applet, it is not fixed because it's not really used anymore. GNOME Shell has it's own network selection menu that does not use the applet. It is the default on most systems, so users don't face this issue by default.