I think I remember the shots you mean--there were a few during HERO, for example: close-ups of Miku sitting on the speaker, I think.
To be honest, I thought it was mostly done for effect, and that those images were probably on the side screens next to the stage (which folks watching the stream would've probably had a harder time seeing, since the camera mostly stays on the stage).  So during the stream, it was cut in for their benefit.
I'm fine either way, really.  I guess I might wonder a little about not having the experience of seeing them again.  At the same time, I appreciated the consideration and the visuals were cool, but having the image change suddenly during the stream was a little jarring, too.  I think I'll be happy sticking with the live camera footage.  Though having the other footage on a bonus disc wouldn't be a bad idea.