Yes, as KMR said the discs in the boxed set are individually the same discs as was sold in the "Collection" and "The Begining" sets, with the exact same menus, eps, and extras. Whoever indicated that there might be any differences in any way had no idea what they were talking about. Like KMR, I know because I own the boxed set.
Where the boxed set deviates is that it also includes the three separate DVD releases: DS Bloopers & Treasures, DS Special Edition, and DS Reunion. That's why it has 131 discs and not just 128.
And as far as the quality in the packaging goes, I'm actually quite satisfied and I don't find it at all flimsy.