From a reading comprehension perspective, people need to read that FAQ again before applying it to encumbrance calculations:
Can you stack armor implants (Dermal Armor, Bone Lacing, etc.), the Armor spell, Immunity to Normal Weapons, etc.? If so, what counts for encumbrance?
For worn armor, only the highest value (Ballistic or Impact) applies, and any modifications to armor (from spells, augmentations, natural abilities, etc.) are applied in addition to those values. Any worn armor counts for purposes of the armor encumbrance rules (p.161, SR4A); implants and magical spells or powers do not.
First off, note that the question is about how to calculate armor, with a follow-up on how to calculate encumbrance.
To answer the "How does stacking armor work with implants and magic?" The FAQ answers:
"For worn armor, only the highest value (Ballistic or Impact) applies..." and carries on to talk about adding in modifications to armor from magic, implants &c.
This is a reference back to "Armor and Encumbrance", page 161 of SR4A, where they explain that if you wear two pieces of armor (say, Armor Vest {6/4} and Urban Explorer's Jumpsuit {6/6}) then you don't add their scores, but take the higher Ballistic armor rating and the higher Impact armor rating (for a final armor of 6/6, you might as well not bother with the Armor Vest).
THEN it answers the follow-on question: "What counts for encumbrance?" with
"Any worn armor counts for purposes of the armor encumbrance rules (p.161, SR4A); implants and magical spells or powers do not."
Note it doesn't say, this time, "ballistic or impact", it says
any worn armor.
If you don't interpret it that way, and instead assume both sentences refer to encumbrance, then you have a contradiction. The first sentence says "combine the best of your worn armor ratings for ballistic with all armor boosts from non-worn armor sources, and do the same for impact". The second sentence says "for encumbrance, only consider worn armor, ignore non-worn armor sources".