You don't have to commit the dynamic tables of course. They will show up on the commit tab, and you can deselect them so they aren't source controlled.
One thing to be wary of is not committing them when they are required by relationships to other objects that you *are* source controlling; as this would cause trouble when another user "Gets Latest" due to dependencies missing.
If these dynamic tables are indeed standalone, then you may want to suggest more complex filtering over on our Uservoice forum
where other users can vote up the request. The filtering in there at the moment is basically the same as you'd get in SQL Compare.