[Jiaz]

Links coming from Extension have different source so you can create Filters in Settings-Filter that work different for local AddLinks/Clipboard vs via Extension.
You can also assign hotkey and enable/disable clipboard monitoring. (You can customize them in Menueditor in JDownloader) Same for browser extension where you can enable/disable clipboard monitoring via hotkey.

You could also setup blacklist in Settings-Advanced Settings-GraphicalUserInterfaceSettings.clipboardprocessblacklist (windows only) to exclude processes from being monitored (eg notepad)

You can also use the info bar extension that offers a drag/drop area where you can drag/drop links into