If you are having this site make individualized touring plans for you, then it is putting attractions in an order that takes advantage of less busy times of the day to get the more popular/slow loading rides out of the way in the morning and/or evening. So, very low wait times are possible- much more so than if you just "wing it" and attempt the most popular rides at the busiest times of the day.
I would still add a bit of time onto these plans- it is very difficult to stay on track and to the minute (bathroom breaks, an attraction not on the list that one of the kids just HAS to do when they walk past it, unexpected ride breakdowns, etc). Overall, though, the wait times can be close to what the site says when you are following a touring plan.
Sounds like you are doing the smart thing and getting your touring done early, then returning in the evening when the big crowds are done. We tour this way, too, mostly. Have a great trip- we have been during the end of October/beginning of November a few times and really enjoy it!