I think that the Maze of Messages from the ARG is a dumping ground of Harley's thoughts that Playtime didn't want. Seeing as he was only kept alive for his usefulness, Playtime probably wouldn't want to have to sift through every thought that passes through his brain. And we know they were certainly accessing his thoughts, as Eddie says "Everything [Harley] knows and thinks is only ever a matter of button presses away."
So what if there were some main- for lack of a better term- folder that collected all of Harley's thoughts? And for everything they didn't want, every mentally-broken thought that was functionally useless to them, there were another folder? I'm not entirely sure how the sorting would be done but I would guess they would be able to do something like tracking how distraught or confused he is when thinking and then auto-sort those thoughts into the Maze of Messages folder.
And as for all of the thoughts we see being specifically from 2002 and being somewhat limited... I mean, storytelling, guys, Mob can't give everything away.