Its up to you whether you use the almond milk at the health food store. If you have skin problems it likely contributes to them. Once you start the diet I would do a week with and a week without almond milk and see if you notice any difference in how you feel. This is the best way to test out a “somewhat safe” food item but everyone is different and you may or may not be allergic to it, etc.
I personally wouldn’t mess with it until you get to stage 3 of the diet and maybe use it as a cheat item once in a while.
And I believe I mentioned this before, but its best to make homemade almond milk and then there isn’t any junk added to it, its fresh, and it’ll contain less molds. The molds are what is the problem and roasting the almonds and soaking them will remove most of the molds. My wife used to make it all of the time and the blending/straining part actually only takes about 5 mins or so.