A 60 minute boil will isomerize nearly all of the hop oils that contribute to bitterness. A 90 minute boil with them in should not contribute any discernable more. The hops added at 30 minutes will have approximately 90% of the isomerization of a 60 minute boil and very little of the aromatic oils will survive that long in the boil. Depending on what hops are used, you might be as well off with all of them at 60 minutes for bittering or move the 30 minute addition to 10 minutes to retain some of the aroma.
A recipe is a record of what someone else did, not a chemical formula. This recipe's designer may not have realized what a 30 minute addition would do. I choose a recipe as a starting point, then modify it to fit what I want from my beer.