Hate to disagree but not always the case. Two examples were it doesn't work.
- checkin in Hel with AY - for some reason onward boarding pass not available, flight not open is normal reason. Get to LON try to SSCI get message 'already checked in'
- checkin with loganair - their system seems only to be able to print two BP one to GLA/DUB other to LON, don't have time in GLA and in DUB can't get third boarding pass, LON-XXX. Arrive in LON try to SSCI again get message 'already checked in'
Sorry I was focusing on Zone R. I am sure that there are some exceptions world wide. As for the AY bit, sounds like they are managing to check you in and the link that generates your boarding pass does not work.