Does anyone know what's up with that? Couldn't find anything via Google. Seems really fishy to me.
Edit: Got the official explanation from the dev on Reddit:
AutoClick Feature of JDownloader works as following. Open the browser and wait few seconds, then take screenshot and search for the Recaptcha click area and auto click on it. Screenshot is needed so JDownloader knows where to click. You can disable this feature, see https://support.jdownloader.org/de/knowledgebase/article/jd-opens-my-browser-to-display-captchas
On Linux, JDownloader creates screenshot to find out the color of tray area so it can try to find it's tray icon and calculate the correct background color for transparency. You see the JDownloader icon having white background. You can disable this via Settings->Advanced Settings->Tray.gnometrayicontransparentenabled
I got curious and looked at the flathub source at https://github.com/flathub/org.jdownloader.JDownloader/blob/master/org.jdownloader.JDownloader.yaml
It downloads the official jd2 installer. So that's not it. I asked on Reddit as well and got the official answer. It's for clicking CAPTCHAs.