I'm sure my concerns are uncommon, but here's my issue. I do various activities, including water sports. I can lock my gear and the ignition key in the top box and lock the box with a combination lock. Sure, someone could break open the box and have the key, but I can be somewhat secure in leaving the bike parked in a public area. Locking the fob in the luggage does nothing, since it's basically the same as leaving a key in the ignition. Also, depending on the type of fob we're talking about, batteries can die or water can damage it. A metal key is dead simple and more rugged.
Just to let you know, there are cheap bags and boxes that block the RFID signal for key fobs. You put the fob into that and place it in your luggage, you are good to go. Or you can be cheap like me and wrap the extra fob in aluminum foil and place in car trunk and you won't have a problem. Batteries can die, yes but there is usually warnings. As for water damage, I usually have a zip lock bag to place cash and things that could be water damage. I know a metal key is 100% more simple but from my past as a locksmith, not really as secure as most think. I just like the convenience of leave the fob buried in your pocket and never having to dig for a key especially with gloves on.