You know, it does sound like Byrne's doing a little bit of a CYA, but it's certainly a justifiable explanation. Interestingly enough, if Chapter One was supposed to be a "Heroes Reborn" type scenario for Spider-Man, I'm surprised they didn't try something like that when the actual Heroes Reborn took place. After all, there were technically TWO Spider-Man running around, so it's possible that one of them could've ended up in the pocket universe along with the Avengers, Fantastic Four, Doom, and the part of the Hulk.
Anyway, the problem with Chapter One was because A. it made some unnecessary elaborations--such as the Burglar thinking Spidey was casing his own house or Peter being caught in the same explosion as Doc Ock and THEN being bitten by a radioactive spider, etc.--that really didn't do expand what Stan Lee/Steve Ditko had set up, and B. the context in which it came out. Remember, it came on the heals of the Gathering of Five, which was a lously way to temporaily "halt" the Spider-Man books. Plus people still didn't get the bad taste of the clone saga out of their mouths, and the reboot (especially how the 616 books attempted to force them to conform to Chapter One and MJ's supposed death) certainly didn't help. It was a classic case of bad timing. Ironically, Bendis pretty much did a "Heroes Reborn" type setup for Spidey in his Ultimate Spider-Man series and is praised to the hilt, while Byrne is vilified trying to do the same thing with Chapter One.