Adobe Premiere can help you to line up multiple audio and video recordings. Look at how to make multi-camera sequences and select Audio to synchronise the clips based on their waveforms:
Is the -stream_loop option actually repeating the input video clip frames to make the loop?
Is there a way to tell ffmpeg to instance the input video frames when creating the loop?
Is this actually a limitation with video formats (e.g. mp4, mkv, etc.)?
For MP4s and MKVs, yes.
If ffmpeg is not sufficient for this, is there some way to create a ...