What experiences do travellers have on using a non-EEA but visa-waiver passport (e.g. US, Australian, Korean) on intra-schengen flights? While ID (passport) will be checked upon boarding, does anyone have any experience with having their entry-stamp checked upon boarding as well?

I have an EEA passport and thus no personal experience, but I am asking for a friend who is legally able to stay in one Schengen country, but is beyond the 90 days period spent in the Schengen area. While I am aware of the legal issues and can understand if some of you advice against this, I'm interested whether boarding staff ever check these details.