The fins or the motor retaining hook are not suppose to touch the pad. If you look in the launch instructions; there should be a suggested stand-off distance. You create this by using masking tape. If it doesn't have one then make should you have adequate gap. If acquired burnt fins, very low altitudes, or static launches because I did not.
As for your your patriot fins; do as you wish. It won't hurt it. It'll help streamline a bit. I do understand your confusion. Some Estes Industries kit instructions tell you to do it, don't say any thing about it, or suggest it as optional. So I say go for it!
I hope this helps.
By striving to do the impossible, man has always achieved what is possible. Those who have cautiously done no more than they believed possible have never taken a single step forward.