Do I actually say to her I know how hard this all is and appreciate you trying to organise?
No! a. She didn't say dictating these terms to you was hard for her--are you projecting? She has to express something for you to listen/validate. She did express she didn't want to spend Christmas with you and you did a good job showing you heard her. b. Why would you tell her you appreciate her "trying to organize" (dictating custody to you)--do you actually enjoy this behavior and want it to continue?