Confused on the new tray icon and dock in ubuntu 17.10 gnome

I can suggest an ugly workaround. Try at your own risk.

• Remove Ubuntu appindicators (not at all recommended, it will remove ubuntu-desktop metapackage) by running

  sudo apt-get remove gnome-shell-extension-appindicator
  

• Install and activate KStatusNotifierItem/AppIndicator Support. It should show most of the app icons excluding electron based apps (Skype, Wire etc.), Thunderbird with Firetray etc. with the correct icon sizes.

• Install and activate TopIcons or TopIcons Plus for the rest of the app icons.

I'm not sure whether installing "KStatusNotifierItem/AppIndicator Support" is necessary. But in my case TopIcons Plus is showing only the app icons not supported by "Ubuntu appindicators" or "KStatusNotifierItem/AppIndicator Support".