Is it important that your column order is sync'ed when getting from source control? We'd definitely consider changing this behavior if others believe that this is the right thing to do. Please join the debate!
Regarding filtering, we're working on specifying this feature now. Could you please describe which objects you'd like to filter out. Would you like to filter these objects so they never reach source control, or would you just want to exclude them from the commit list?
Red Gate Software