Modernizr will include those prefixed styles in its detection, so yes, you should keep them.
If you drop them, then your site will break because browsers which require a prefix will be detected by Modernizr as supporting the feature and thus and won't run the javascript code, so you won't have the style at all for those browsers.
The Javascript code will only be used by IE7* or earlier, where the box-sizing
style is not supported at all.
(* ...or other really old browsers like Opera 9 or Firefox 1, but realistically no-one is using those)