I'm sorry, with respect that comment is a load of rubbish! Which albums - 'all the way through their career' - did it hurt? Name names!
If SFF and Penny Lane were to be included on Sgt. Pepper, they would not have been released as a single. It was very common in those days to not include the current single on an album, and it wasn't just the Beatles or EMI, it was across the board. So which album was hurt?
Hope I'm doing this reply correctly.
Blue, perhaps "hurt" is a tough concept to deal with, since their albums were so near perfect. But think about having the singles on the albums. What album wouldn't be helped by She Loves You, I Want to Hold Your Hand, etc.? We Can Work It Out? Day Tripper? Keeping those off albums was part of the times -- I'm not arguing that -- but their inclusion helps any album.
My point was, Pepper, cultural landmark that it is, could have been better by adding Penny Lane and SFF. I'm sorry, but that's a fact.
Someone else can tell you which albums the singles would have gone on, because I don't have the encyclopedic knowledge of recording sessions/release dates.
But reverse engineer it, for a sec. Imagine a White Album with Hey Jude, Lady Madonna and Revolution, and make the argument that it would've been better with #9. Good luck.