Well they fully acknowledged it's not a desired behavior and apparently they plan to fix it:
"Posted by Microsoft on 9/23/2013 at 3:03 PM
Thank you for bringing up this issue. Unfortunately, this functionality was lost when the web project properties page was refactored. We are working to get this feature back into the product.
For now, if you have a project with this setting unchecked in VS 2012, and open it in VS 2013 it will respect your individual user settings until the first time that the servers section is modified on the web project properties page."
"Posted by Microsoft on 9/23/2013 at 3:03 PM
Thank you for bringing up this issue. Unfortunately, this functionality was lost when the web project properties page was refactored. We are working to get this feature back into the product.
For now, if you have a project with this setting unchecked in VS 2012, and open it in VS 2013 it will respect your individual user settings until the first time that the servers section is modified on the web project properties page."