Technically speaking, I believe the Astral Skin would be on the outside of any worn armor (just like the Astral Armor and Astral Juggernaut do), but would not interfere with the armor's function or abilities in any way, and neither would the armor interfere with the Astral Skin in any way (excepting that the armor bonuses and similar effects wouldn't stack). Referencing your rules quote:
Psychoactive Skins: A deployed skin completely covers the wearer and all his equipment like a second skin, allowing the wearer to see, hear, and breathe normally. It rolls away from various parts of the body as needed, such as when the wearer needs to eat or access a backpack. Held items or items specifically excluded are not covered by a psychoactive skin.
The phrase "all his equipment" would include worn armor, especially taking into account the mention of a backpack, which would be worn over armor. There is, though, no real reason that it just fits to the wearer with armor, backpack, etc over it. Though the wording "when the wearer needs to eat or access a backpack" opens the question: can the skin prevent others from opening the Aegis's backpack?
To respond to one of your comments on @KRyan's answer, as well, worn armor will not interfere with Increased Size or Improved Increased Size:
Increased Size: The astral suit grows in size and the aegis and all of his equipment is treated as one size category larger as if affected by expansion. The aegis must be at least 9th level to select this customization.affected by expansion."
Expansion: This power causes instant growth, doubling your height, length, and width and multiplying your weight by 8. This increase changes your size category to the next larger one...
All your equipment, worn or carried, is similarly expanded by this power.