First, I thought it was pretty clear that HDYS is directed at Paul. John has said so himself although later self-analysis made him reflect that he probably actually wrote about himself using his animosity towards Paul as a base.
And no, I don't believe there's any connection between LSD and the Sgt Pepper line. In fact, I don't understand the confusion. Paul originally saw Sgt Pepper as a concept album but, except for a few songs, it really isn't. The end result probably took Paul by surprise. The public's overwhelming response to it probably also took him by surprise. To this day, slap it if you must, it's still considered one of the greatest albums of all times.
My hunch is the song's being over-analyzed. As said, the lyrics are such a hack job. We do know that some of them were changed considerably before the song ended up on the album. Toned down to avoid libel suits and the like. That mother's eye line have the feel of being altered, which generates special problems in song lyrics where you want the lines to rhyme. So whatever written had to work with the 'surprise' in the preceding line, although 'mother's eyes' isn't a very good one - except for having the required number of syllables.
Sometimes I dream in colors
It always happens when
I find myself with others
Who don't pretend