Video displayed in Waveform Editor
Re:Video displayed in Wave Editor. When you apply processing - a new audio file is created disassociated from the video. I would prefer option to replace the source audio with processed audio - and export via video pass-thru to prevent re-encoding.
In the most recent release, you can view video files while editing the audio stream in the Waveform view, without needing to place it into a multitrack session first. However, as you noted, saving does not currently write the new audio stream back to the original video file, relying upon Adobe Media Encoder to create a new file. While AME can support smart rendering for many formats which support it, not re-encoding a video stream, this isn't yet available for all formats and does require additional steps.
There is an open feature request in the backlog to support this request already. I will add your notes to the item.