The expression isn't about noticing a thumb because it's sore, it's worded like that because you wouldn't be as likely to bend a sore thumb, so it sticks straight out. It's a play on words.
Whenever I hear that saying, I always pictures a cartoon characters thumb after being hit by something. Where the character is running around and their thumb is huge, red and pulsing...
i had a sore thumb.... no one noticed :(
Or it could be talking about the way you notice it a lot when youre the one with the sore thumb
Maybe over the years it got twisted like a chinese whisper? Sticks out like a sore bum in an under 12's church choir was the original.