This relates back to my sports bike days, when alarm remotes weren't alway totally waterproofed effectively - I got into the habit of using a lanyard around my neck that would tuck inside one-piece leathers.
So, all the ancilliary keys/fob/remote go on the lanyard ring - then the bike key alone has a simple loop/leather fob which just clips to the lanyard when not in use. When on the road, there are no sundry keys to rattle about/cause damage. The lanyard can be worn around the neck, tucked under jacket, or get attached to a dog clip in your pocket.
Works for me, just one of many solutions I'm sure.
Ride Safe .................... KEN