You are just speculating
1. The btn to add or remove features to a site doesn't save site settings so it can't affect permissions
2. of course the btn for saving site settings does set the site permissions to the values from the checkbox lists, nothing erroneous about that
3. The role binding was called from PopulateControls which is not called on postback and there wasn't anything erroneous about it
4. All of that is moot because you are looking at old code, in the latest code the permissions are not in site settings
I have no explanation for what you are saying is happening but no-one else has reported it and I was not able to reproduce it and I don't think it was a mistake in the previous code, but as I said that stuff is no longer in the site settings page at all. My advice is to upgrade.