Most variation between populations is not so much what genes are there, but how at what level they are expressed, point mutations, and short repeats (all of which are unlikely to create totally new structures). For there to be a population that had spike protein expressed, there would have to have been some sort of horizontal gene transfer into the germline (which is relatively protected from mutations for precisely this reason) at some point in the past. There’s reasonable atlases of human genetic variation (see, for example, the 1000 genomes project), so if there was some large population of people with any obviously new viral sequence, we’d see it.
Plus, if a person somehow, miraculously, had a protein that looked like Spike, their immune system should already be tuned to ignore it. (I have a PhD in biology, but immunology was not something I have much expertise in, so take this with a grain of NaCl).
I'm not very worried about it. I just received my first dose of the Pfizer vaccine today(some soreness at the injection site and fatigue ~12h after). I just would like to hear the response to that concern in case someone tries to argue that angle with me.