If you use a subtitle (or similar) as a watermark, it can be easily removed. So why should you watermark at all? So the answer is probably no.

Well, I am making a live Youtube stream with audio and wanted to add an album cover on top for the track when it is playing.

I don't believe that's possible with any tool since you're changing the actual video content?

I know some services do this somehow, so I was thinking maybe there is a way in ffmpeg.

Hmm. Example of such a service? Wonder if we can reverse engineer it.

One that comes to mind is this AMCDX Video Patcher [1] made by Alex Mogurenko. I've played around with it and it's very cool. There is the frame editor to overlay a PNG or file to file where you can insert all or some of another video over your target file. I haven't used it in production but I've played around with it. The file to file tool seemingly only touches the effected blocks of video and there's no rendering. I just did a test where I was able to cover a persons face with an image. Alex has a video showing him blurring a section but I think blurring option was removed in favour of being able to overlay an image. [2]

The video needs to be Prores and I'm not able to guarantee it's not touching any other part of the frame but it feels like it's just the effected section of the video frame that is getting changed.

If you are trying it out make a copy of your original video before you start, it does the edits in place.

[1] https://mogurenko.com/2021/01/29/amcdx-video-patcher-v0-6-7/ [2] https://youtu.be/T-EJRB-xAdU?t=44