Yes, the Touring Plans software takes advantage of the grace period, although I usually hear the recommendation elsewhere not to rely on it.
However, if you don't like running into the grace period (which I never do), you have two options:
1 -- simply swap the "graced" attraction with the one before it and hit 'Evaluate' instead of 'Optimize'. This will calculate the times based on the order you have the attractions in instead of giving you the one that TP things is the least time. I usually tinker with my plans some this way after seeing the best plan that TP has to offer. I think the software is great, but it just doesn't always think about touring the parks the same way I do -- if I swap something and the difference is only 3 minutes but I like it better ...
2 -- Leave the steps as they may but put a note on the previous step to do the 'graced' step first depending on time. It's not uncommon to find yourself running ahead of schedule, so you may find that following in the recommended order doesn't even have you arriving there in the grace period even though your printout of times says that it will. If you leave it in the recommended order and make a note, you can decide on the fly.
