That is partly true. I'll try and be brief and simple. If you upload an image via the media tabs, an activity is created for the image. The comments are actually the activity's comments. When you use the activity uploader, an activity (hidden) is created for the image and there's a status update that contains the image as an attachment.
So when you comment on the activity here, you are commenting on the status update, not the image. However, when you comment on the media, you comment on another activity, not the status update.
Why is it this way? Simple. Try uploading multiple images in the activity upload and see if it makes sense. Also, try doing similar things on Facebook.
We know it is patently weird and we are trying to do this another way, probably get rid of the activity dependence of media comments. The way activities and comment notifications work in BuddyPress is actually a pain for us. There was some talk about a unified activity stream, but I guess, it'll take ages for that to work.
We are on it, but. And we'll find a solution.