Add some more checkings to the DiffEncoder.

Check that we don't attempt to use the region outside the old file.
While this is supported by our decoder, there's no reason why we should
do that and it often means a bug in the encoder.

Bug: None
Test: Added unittests that would fail without the fixes.
Change-Id: Ifd6d8763ae4e6b3f29a5a1289f22900a278dd1b0