Regarding the change in bundle format, the change isn't drastic. It appears to just be some more values in the header and using longs instead of ints for certain addresses in the header of the db and bundle header. I'm curious as to why they changed this, because it doesn't seem necessary, especially considering many of the values changed to longs never go >100. It's a possibility that the format change may be the cause for the mod_override issue, but it's more likely that it is an engine side thing.