Should've asked this way earlier. My idea for the jam has a protagonist whose queerness isn't entirely relevant to the story; rather, the themes and concepts of the story are allegorical to lived experience in my life directly related to my queerness. Is this, like, okay? Or does my story have to be explicit and obvious in the ways it is queer? 

Yes, it's absolutely fine to approach the prompt like this. There are many ways to tell queer narratives, and there is no reason to exclude allegory.