Armor-ignoring effects probably do not ignore racial armor.
The Rulebook has no explicit guidance here, but there are two caveats to wearing armor that logically should not apply to racial armor:
Characters take penalties for sleeping in armor (p. 156). If natural armor were equivalent to normal armor, crawns and ishiris would always be subject to this sleep deprivation penalty.
Attacks against unarmored targets get a to-hit bonus (p. 135). Crawns and ishiris would never count as unarmored targets due to their natural armor.
A final piece of evidence is in the "Make Your Character Adventure". If your quiz results make you a crawn, then you're instructed that (p. 61):
You get a +1 miscellaneous bonus to Soak Rating because of your scaly skin.
Likewise for the ishiri, p. 64:
You get a +1 miscellaneous bonus to Soak Rating because of your rocky skin.
So these bonuses would seem to go in the "miscellaneous" blank in the Soak calculation, not the "armor" blank.
Considering the above, it seems likely to me that the "natural armor" phrasing is just flavor text that isn't meant to affect the game mechanics.