It's not a bug... It's never caused anyone any problems. Ever. In fact, it is intentional behavior of the IDE and the migration process. All that says is - this datawindow is written to the "version X" specification, so it will not contain any code constructs from later releases. So, for example, a "Version 4" datawindow will not have XML templates, but it will run perfectly fine in 12.6. As soon as you open the datawindow and edit it, it gets stamped with the current version string.
There is absolutely no runtime functionality that's based on this value whatsoever. Despite what you claim, you've never found compile or runtime errors because of this... Whatever may have happened, it was not related to the version number string in the dwo source code.
Let's just put this non-issue to bed, shall we?