But can you still seek on a video that's being instantly transcoded? To be honest I don't know if anyone does that except YouTube, and it jumps to the time so theoretically you have about a second or two when the request comes into pull the file and start encoding. It sounds like the mezzanine file is chunked, so the time to pull it down is pretty fast.
Since it's your own player you can hint to the backend.
Do you dynamically generate the manifests too? Or do things get transcoded on request?