Probably not to piss off the Lithuanians more than they probably already do. Though actually, I don't see why the Germans would care. I mean it's kind of unrealistic for a German WWI Victory Alt-History to not have Lithuania and Poland be annexed into the Reich, but I guess it's to not screw over Lithuania and Poland more than they already are at the start. So that's a reason I guess. Plus if I remember right, Lithuania had a lot less Germans than the other Baltic states historically.
An independent Polish state was already discussed, and I assume Lithuania was going to be independent anyway.