This has annoyed me for too long. Here's how you remove the duplicate in the taskbar.
Open the Konsole adn type;
mkdir -p ~/.local/share/applications/
cp /var/lib/flatpak/exports/share/applications/com.google.Chrome.desktop ~/.local/share/applications/
kwrite ~/.local/share/applications/com.google.Chrome.desktop
add:
StartupWMClass=google-chrome
under where it says;
[Desktop Entry]