Hi, sounds like an interesting project. I'm not too sure what's best though, if you don't want to split the tracks then all I can suggest is some big bold text at the start of the game description. Just a sentence explaining that only 1 track is for this jam. Not sure itch offers any alternative to that.
Viewing post in Question about suitability for submission
Ah, I asked about this on the itch.io discord and someone suggested that the jam could have a custom submission field that anyone can fill in, so for example a field like "What has been finished?" or "How long has this been sitting around?" or the like could be helpful, even for normal submissions. :)