In these cases, no, they wouldn't be thrown out. The aim is always to accept accessibility changes but they still need to be tested first, just in case they have negative affects which would need further investigation to be fixed.
Hi, I wrote HTML5 Bones and to be fair Simon has a good idea (detailed in the GitHub pull request) in that there should be two versions, a file with all the comments and one without - and so catering for both types of users.
I definitely don't want to remove the comments as they are integral to what I want the "template" to help people do.