I do not know the history of the 48" max frame length recommendation on the Mini-Max, but it was changed to 62" at my suggestion a couple months ago. The people at Hyside are a great bunch, I'm sure they were passing on the best information available to them at the time. They (as most, if not all, boat manufacturers) do not build frames in house, so there might be a gap between design intent and what current frame builders are actually putting on their rubber (or plastic.)
Can you post a pic of your frame? You mentioned home made, if speed rail/similar was used it might be easy to add a removable front bay and have the best of both worlds...day and gear setups.