Honda thought that through (regarding dead key fob battery), good for them. It would appear that for the GL one must still have the key fob (the key inside the key fob) to get the bike running for Honda's procedure. So don't lose the fob. No different than don't lose a mechanical key on a wired ignition.
On my RT, if the key fob battery is dead or fob is lost, I can use the bike's plastic 'valet' key (which has a RFID chip imbedded in it) and position it into a very specific place on the bezel of the instrument cluster--the bike is able to read the key there and enable the ignition. Just as the new GL, if you're a long way from home and lose the fob, you've a problem. So I carry both the fob and the 'valet' key for my RT.
Due to their size, I believe the key fob is harder to lose than an old-tech mechanical key. But as a bit of added insurance, I have a bright yellow lanyard attached to my fob, and I carry it inside a zippered belly pack.
My RT keyless ignition is a very-much-appreciated feature! I'll take it any day over a mechanical key as I found myself too often fully suited and gloved searching for which pocket held my ST's key.
Also, I assume that with the GL (just as with my RT), the key fob should never be stored near the bike--it communicates actively with the bike, drawing power. When I bought my RT, the consignment shop didn't know that and had stored the fob in the bike on the showroom floor--the bike's battery was depleted. Further, the fob battery was drained and required a new battery a few months later.