Remember the note
Thoth is another deity we encounter, back in Sub6.- I think you're ready to enter the Submachine. You know more than enough and will probably find out more on your journey. Remember, this can destroy or transform you. But you will not return the same man. May the wisdom of Thoth guide you.
- Thank you, holy usher. I will not fail you.
- Don't fail yourself, my young disciple.
The interesting thing about Thoth and the color green is, he wrote things on green emerald tablets
http://www.bibliotecapleyades.net/thot/esp_thot_1.htm
You can read about it there
Take notice of this line
In later times, the descendants of these guards became the Pyramid Priests, while Thoth was deified as the God of Wisdom, the Recorder, by those in the age of darkness which followed his passing. In legend, the Halls of Amenti became the underworld, the Halls of the Gods, where the soul passed after death for judgment.
So my theory is the flag colors have religious meaning pretty much.