I can understand that with normal loading of the bike then everything on the lowered bike starts off closer to the ground, so there is a slightly higher possibility of grounding something in extremis. However I don't think it's as bad as it seems, as for example with the self leveling suspension, if we assume for arguments sake that the bike adjusts to provide a loaded sag of about 1/3 of the available suspension travel, then the loaded ride height of the standard bike will not be 20 mm higher, but only be 2/3 of 20 mm higher than the lowered bike - so about 13 mm difference.
I can't remember the exact figures, but if the standard bike has 200 mm maximum rear suspension travel and the lowered bike has 180 mm, then the loaded suspension figures with 1/3 rd compression should be 133 mm v 120 mm.
I also read that the lowered bike has slightly stiffer springs so that it uses up a little less suspension travel for any given load than the standard bike, and so should be no more prone to bottom out the suspension. In the case of road or off-road conditions which cause the suspension to hit maximum compression and bottom out, then there should be no difference in minimum ground clearance between the two.