Probably to head off inevitable complaints by people assuming that this is a criticism of those sites' designs.

The 'complete redesign' trend has been seen by some in the design community as a bit arrogant and impractical. My guess is that poster didn't want to be included in that crowd.

Perhaps as a "I'm not committing contributory copyright infringement" statement.

Altering a page for a user to remove ads, for example, is pretty much providing a [unlicensed] derivative work. Providing the tools to perform copyright infringement - with the encouragement of a demonstrated technique - could be considered to be contributing to a tortuous infringement, jurisdiction dependent [along with a pile of other dependencies] of course.

I thought it was a good idea to include the disclaimer. As obvious as it might seem that these are opinionated modifications to the site's intended style, it may save some grief to make your awareness of the issue clear.

Probably doesn't want to burn any bridges or piss anybody off. If he's friends with Mark Otto (creator of Bootstrap) I assume he's not some unknown CS student looking to make a name for himself but actually somebody who works in the industry and cares about his reputation.