No but I thought there was height requirements for openings like that.
If you're talking about a shed, I don't think there is, but I could be wrong. Ask your building department if that's an actual constraint before racking your brain trying to figure out a way around it. I'm not sure how you would flush mount a rafter end to a beam in a way that is structurally sound (i.e., would pass code, whether you'll need to or not). I've not seen any Simpson hanger for that application, but then again I don't know their entire product line.