Currently this isn't possible unfortunately. We only really look at object level settings rather than server level.
There's an existing feature request for the SQL Compare engine to support this, but I'm not sure if/when it's likely to be implemented. If it is, then potentially SQL Source Control could take advantage of course.
If the feature is important, please feel free to suggest it on our Uservoice: http://redgate.uservoice.com/forums/390 ... ce-control
It's a good way to gauge if a lot of other customers would find the feature useful, so things can be prioritised appropriately.