Well, I wouldn't say that the free base form is more potent, it's just missing the HCl which means it is going to have to rely on your stomach acid to get it. The HCl salt has been called "predigested" before, but what's more important is that it is highly water soluble in this form. If it is highly water soluble, more can be absorbed much faster, and that may work out to be "more potent."
It is likely that the density of the powder will be different (free base forms tend to fluff). In my opinion, the HCl salt is superior, even though it makes the molecule weigh just a little more, so you end up with less per gram.
Also, free base forms of
amino acids tend to REALLY stink.
You should send this question to Mike if you really need to know.