No, it means that PPP-System does not count as separate pieces of armor (ie, stacking), but rather modify your armor rating prior to determining encumbrance, just as helmets and shields modify armor prior to determining encumbrance.
There is nothing I can find that says the PPP System doesn't count towards encumbrance.
Example:
Body 3 character wearing Armored Clothing (4/0) experiences no encumbrance, since 4 < 3x2.
He then straps on SecureTech PPP Leg/Arm casings (+1/+1), Helmet (+0/+2) and Vitals Protector (+1/+1) for a final armor of 6/4. So he's still not encumbered( 4+1+0+1 < 3x2).
Picking up a Ballistic Shield (+6/+4), he immediately wishes he weren't so stupid... he's taking a -3 penalty to Agility and Reaction[4+1+0+1+6 (12) > 3x2 (6), (12-6)/2 = 3].