Peace, Love, and Butterflies! We have a 2e child also (but instead of ADHD he has autism) who has similar problems.
I, too, was trying to determine which were due to the gifted OEs and which were due to the autism, but have since given up since the whole package is intertwined. The main thing is that we all work together to help DS have appropriate behavior in the classroom. It doesn't matter what his over-reaction to something minor stems from, but how he can overcome it and get back to doing what he is supposed to be doing with the rest of the class.
Truthfully, I think a lot of his accommodations that he has in place due to his IEP for autism help with his OEs, but I am not going to say that. Do they let you make an IEP for gifted OEs? I don't know and I'm not going to ask to find out. The good news for us is that since he was diagnosed with autism very early (age 2.5) we have had 5 years to work on appropriate behavior...and it has been a LONG road with lots of specialists and therapies.
DS's behavior is not perfect, but I keep thinking what his teacher said this year: he is not her biggest problem. Woo hoo!!!
Anyway, to answer your question, if the behavior is disruptive to the classroom or to your child, I think it should be addressed and not ignored or "accepted." Behaviors that make our DS stand out too much really end up causing him anxiety and turn into a vicious cycle leading to more problems and disliking school.
Nan