Actually if you slide in 1/8 fiberglass rod ( I just used kite rod that I bought at walmart (I bought a kite kit and stole the rods from it) into the trailing edge seam on the upper portion of the Hobie kayak sail it still furls just fine.
However you are correct adding fiberglass rod into the lower seam requires the rod be removed before furling the sail.
As an alternative to the fiberglass rod on the lower portion I have had pretty good success using a standard 1/2 inch wide steel tape measure (the kind that's 1/2 inch wide with a slight curvature (available at any hardware store). My 'used to be' 16 ft tape measure is now an 8 foot tape measure ( LOL).
In order to get the tape measure into the sail it requires sewing on a larger pocket along the bottom edge (which is actually pretty easy, and can be done by hand, or with a hot glue gun). To protect the tape measure from the salt water I just cover the steel tape measure with 3M packing tape, if you dip the end of each steel batton in epoxy (to make a smooth ball shape on the ends) it won't cut into the sail as it slides inside the pocket.
On the Hobie kayak sail it might require 2 separate tape battons, so it forms a () shape. This will furl and unfurl with no difficulty, and should provide a much better sail shape. Make sure you make the tape batton at least 2 inches shorter than the pocket so it can slide freely in the pocket, otherwise it will pop out the back of the pocket when you furl. It works best to cover each tape individually, then just slide the tapes one at a time into the pocket so they form a () shape.
Just food for thought
It's best to use a brand new tape measure (I think they are around $7 bucks at Home Depot) with no scratches on the special protective coating, and during construction try not to scratch the surface or the edges. Using an old scratched up all worn out one didn't work out so well. To cover with packing tape I just pulled a long piece of the 2 inch wide 3M packing tape, placed the batton in the middle and folded over one side then the other over the steel tape, trying not to create any bubbles in the mylar tape coating.
Here is a pic of my old Oasis (taken in and around around 2007) showing the sail furled with the stuff described above installed into the sail and the sail all furled up (at least I think I had all that stuff installed at that time this pic was taken, can't remember for sure) using a home made furler (Hobie now sells a nice furling system, which I recommend). I don't recommend some of the other contraptions shown in the photo, most didn't work out so well (LOL).