I once applied for a job at medium-sized startup, passed their phone screen, take home assignment and onsite, and then had a meeting with the CTO where I was told that they have had problems with ex-Googlers before, and then was rejected after that conversation.

That seems like a very narrow minded approach. I’d be concerned about applying to that sort of company just by hearing that they apply nonsensical filters like that. Can you give some examples, since you claim there are multiple?