Think of site  definitions as a burned CD - once you create them you should never modify them - doing so can have VERY unpredictable results with existing sites (depending of course on the nature of your modifications). Also, modifying those files is unsupported and will result in you losing support from Microsoft (of course from a technical perspective there are modifications that you can safely make but the loss of support is generally enough reason to not do it). And finally, any changes you make can be overwritten by service packs or hot fixes (unlikely but...).