Save it in source control. Add the three or four extra lines of code it takes next time the structure is expanded. I think without some marker it will be hard to track what database files have been upgraded and which havn't. In this case a version number is the simplest thing. If you could encounter skew between program and database versions then including some sanity check is something you are going to need.
Extra space smells bad.
Since you will have to deal with the issue anyway I would concentrate on making sure that adding and changing fields was an easy thing to do. Refactoring is good. If you know what will be added add it now. All rights reserved.