First, you can already disable notification list per app if you don't want them and you can also disable notification bubble if that's the one bothering you.
No, I don't want to disable notifications for apps. They are not bothering me. Just the double dismissal thing grinds my gears.
Then with your concern of "already interacted with so shouldn't be listed anymore", I think the use case of it is you mostly dismiss notification bubble to attend to them later on so it makes sense for them to still be listed in the notification list.
For me id doesn't make sense. If I dismiss it, that means I've allready read it (notifications are really short) an I don't want to see it anymore. If you want to see past notifications there should be some history option in the notification tray, or somewhere.
One thing that comes to mind to probably have a way to "dismiss to check on later" and "dismiss permanently". Perhaps a swipe to the left or right for these 2 options? can't think of a way for mouse though.
Yes, this could be also a plausible way. Adding it to "pool"
You also mentioned clicking on the bubbles or some buttons. That is supposed to open the corresponding app and the app should handle clearing out the its notification from the notification list. So if you see apps that doesn't do this then you should log an issue to their respective repo.
No, I don't mean the buttons in system tray notifications. I mean buttons in notification bubble. After every SMS a get a notification about my credit and if I want to save the message. There are 2 buttons Save and Cancel.
My point is this. I'm writing multiple messages. After each sent SMS I get a notification about my remaining credit and if I want to save the credit message. I always hit Save (or Cancel) and continue writing other messages. After last message and crdit notification, I put the phone to stand by mode. Afer a while I see green notification light blinking and I think that there is an response. But not, it's all the previous credit notifications I interacted with.