It does however effect you if you delevel and suddenly can't use the gear you have equipped. Found this out when I dropped below 25th level with some 25+ gear on. It unequips it for ya on respawn. So at lower levels it must see something it thinks is too high for you to equip even if there isn't anything. I too have had it happen to low level toons that only have starter gear on.
I would hazard a guess that its the subrace/player/faction skins that are equiped on you. If you have played with the toolset you know that there is an invisible second layer of skins that can be applied, and we do.
In addition to Leto thats how you get some of those nifty bonuses.
*Computers are alot like air-conditioners. They work great until you open windows*