It would be nice if there was the option to use an alternate icon for the tray that's simpler. This feature is common on some Linux desktops (eg. KDE Plasma and Gnome), where it's known as symbolic icons.
Such an icon could look like the following, adapted from the regular icon:
Changing the icon in the tray seems to be simple; the relevant line of code is here.
(Currently, Joplin is the only thing regularly on my tray that doesn't have a symbolic icon, and I don't like how much it stands out...)