So glad to hear it went well and they are willing to work with you.
My older dd, who is also an anxious child, went to a school starting in kindergarten where they used the color system. There was only 1 time she wasn't on green for the day and it was b/c I didn't return her progress report signed the very next day so they put her on yellow for that. Other than that she never had problems with being on any color than green and it still created anxiety and angst for her. She also had difficulties with anxiety with choosing what she would have for lunch, or who she would sit with. The whole ride to school she would agonize over it and cry that she didn't want to go to school b/c she didn't know what choice to make. I tried explaining to the school how anxious she was but b/c she didn't show any anxiety at school they didn't believe me. That school did more harm than good and I should have pulled her out when I had the chance.
She is in a much better school (doesn't use the color system) and her anxiety level have decreased dramatically since the beginning of school last year. FWIW she is dyslexic as well.