I did. I try to remove all internal fixed stresses from parts before final installation. I think that’s a good practice. Look at Section 5 where it describes how to use a vise and non-marring hammer (I have a cheap harbor freight orange plastic dead blow hammer for the purpose).
Don’t over do, there is work hardening and fatiguing possible but it would be best if all parts lay on one another without much force at all to get a a flat result.
That being said I’m sure there are many places (maybe this one) where it doesn’t matter so much.
Rather than figure out whether it matters and how many years it will take before fatigue fractures, I just straighten everything.
Bear in mind many parts are supposed to be not-square. Flanges often should be angled for instance. But squared up to the skin they are holding every time.
Good luck! I think this part is fun.
