This question comes up frequently and if we had a "Urban Legends" section, it would be at the top of the list.
The majority of contributors to this discussion topic on the Discussion Page have agreed that this is not a "bad thing".
Here are some of the reasons:
1. It provides flexibility for altering pickups (e.g. installing a full size humbucker in a Legacy).
2. There are tonal benefits (more airy sound).
3. Other guitar builders use this method and have stated similar positive reasons and results.