The above link to Navy website contains the phrase ' Furthermore, under the law, the principal standard for deciding on a time zone change is the "convenience of commerce." '.
This makes it clear that the actual boundaries have more to do with commerce than any thing else.
Northern Indiana has most of it's commerce with the Chicago area so it makes sense to share a common time.
The Upper Peninsula of Michigan is supposed to be in the Eastern time zone to match the rest of the state, however each county that directly touches, and trades with, Wisconsin is in the Central zone.
