Skip, Can't provide any answers but maybe some things to consider:
1. If he were selecting the school without baseball as a consideration, which would he prefer.
2. With baseball involved, what opportunities will he have to play as a freshman at the DI vs DIII?
3. Which coach and team felt best to him? Hopefully he has visited both schools, watched practice, stayed with the team and has a good feel for which he prefers.
4. If, for whatever reason, he does end up liking the choice he makes, it is much easier to transfer and play going from DI to DIII rather than DIII to DI. If you can believe it, the NCAA actually precludes a DIII player who transfers to a DI from receiving athletic financial aid in the first year after the transfer.
5. And perhaps most important...which has made it the clearest that they want him. A coach who says "I want you" and who tells you where you fit, and goes the extra mile to let you know those items is telling you something very important. It is a message I would listen very carefully to make sure it was sent and heard.
Good luck. Let us know the decision.
Also, remember, it is great to have a decision. There are lot of real nice players out there who don't have the option at this point.