I wholeheartedly agree with the OP. ModernMix is an amazing piece of software. But I've got about 50 clients running Start8, none of whom want or need ModernMix. These same clients are very likely to plow right through the update dialog box without even noticing the "Also install ModernMix" checkbox.
Instead of an easy-to-miss checked-by-default checkbox, it would be much better to have a proper dialog box with a "No thanks. And please don't ask me again" option.
At the very least, a registry key to supress the checkbox would be very handy for admins such as myself.