There is an existing ticket #1103 which has been closed but the issue has not been fixed. I already have the extension KStatusNotifierItem/AppIndicator Support installed but after reading about Tray Icons in that ticket I installed it also. It has been mentioned that although this extension enables the option to hide window when starting cryptomator it creates a black icon in the panel, but that is not the only issue. Crytomator is also permanently in the dock or launcher, and for some reason I have a tiny cryptomator icon top left of my destkop.

I know that Gnome made changes to the panel and tray in Gnome 3, and from recent experience that starting Cryptomator hidden works perfectly in the MATE desktop environment, but Gnome is the most widely used DE on linux, and other programs like Insync have a working tray icon without the Tray Icons extension, and without the issues I have mentioned.

Everything I have described about both Cryptomator and Insync are in this screenshot.

Crytpomator is amazing, and none of this will stop me using it, but it will bug me so please implement a solution.