My solution to this is very simple. There are no other keys on the key ring with my ignition key. I also leave my "naked and alone" trunk key (not on a key ring) in the trunk all the time except when the bike is parked anywhere besides my garage. With the trunk key in my Givi case, it can't fall out when it's turned toward the unlocked position. When I park, I lock the ignition key in the trunk and put the trunk key in my pocket (except for the rare occasions when I absent mindedly put both keys in my pocket).
(Edit) Added note: When I sold my Suzuki GS850 a few decades ago, I had discovered that the ignition key could be removed when it was turned on and the bike running. That was never an issue for me, as it never caused me any problem, and I didn't think to mention it to the fellow employee where I worked before he bought the bike and rode it home. He put the key on a key ring or chain that had his house key, office key (and likely more than that) and rode home. When he arrived home he discovered all his keys were missing - they had bounced out of the ignition lock cylinder somewhere along the way and were laying in the road or in a ditch. I don't know how he shut the bike off as I never asked, but I assume he was clever enough to somehow remove the side cover hiding the fuse block without raising the seat, then find the main fuse to disconnect everything electrical.