It does seem likely to me that the second version of the set is the one without the specific mention of Pet Peeve and Southbound Duckling, since these two films turned out not to be on the second volume at all. Sounds like the kind of mistake that would be very logical to correct for a second pressing.
What I find interesting is that, for whatever reason, these two cartoons are specifically singled out as not being "enhanced for widescreen TVs". As far as I know, "enhanced for widescreen TVs" in this context means, presented in anamorphic widescreen rather than pillarboxed widescreen. Perhaps this is the reason these cartoons were apparently pulled from Volume 2 at the last moment and instead ended up on Volume 3 -- where, from what I know, they were presented in proper anamorphic widescreen.
By the way, I'd imagine one simple way to find out if you have the first or second version is to check if the cartoons on your copy of the set are unedited or not.