Meth.HCl is actually more damaging to your body, the HCl salt damages the lungs or mucous membranes, FB meth is fine.
Have you actually tried smoking the freebase? From SWIM's experience, the freebase is almost painful to smoke, while the HCl salt is smooth and almost tasteless.
From my hypothesis, the freebase is more damaging to mucous membranes, as it is quite caustic in aqueous solution (ph 9.5), while the HCl salt is almost neutral (ph 6).