There is a halachic principle which states that food that would not be consumed by a dog is not halachically food. Since chocolate is toxic to dogs, do we actually need to worry about its hashgacha?
The halacha you're citing is not a leniency that whatever is harmful to dogs is not food. It's a stringency that, even though chametz is no longer fitting for human consumption, as long as it remains a suitable feed for animals such as dogs, the prohibition applies. Anything which is considered food for humans doesn't even enter the discussion.
Inasmuch as I believe @loewian's answer is the correct answer, I would add that according to one approach (this is the approach taken by Levushei Mordechai siman 86 and Divrei Malkiel 4:22:6, and accepted as Halacha by R' Blumenkrantz (of the publication "The Laws of Pesach")), the halacha of "would not be consumed by a dog" is only applicable to a food which once was fit for such consumption and degraded to a point of inedibility. A food which was, by its nature, never edible by a dog (which would describe chocolate according to your argument) would not be included in this category.
Additionally, the Rosh (Pesachim 2:1) rules that even if something is degraded to the point of not being edible by a dog and therefore does not require to be gotten rid of on Pesach, still one is not allowed to eat it, because by eating it he has shown that he validates it as being edible and its status is reinstated. So this would not even potentially help for eating non-Kosher chocolate.