Hi purestmattress,
I’m glad the information I provided was assistive to you. 
Without knowing the specifics about any particular brand, cover or product you were considering, I can offer some general information that I think will help make things a bit clearer for you.
First, there is more information about the three different levels of organic certifications in post #2 here and some of the benefits of an organic certification in post #3 here and there is more about the different types of organic and safety certifications in post #2 here and more about some of the differences between organic and safety certifications in post #2 here and there are some comments in post #42 here that can help you decide whether an organic certification is important to you for environmental, social, or personal reasons or whether a “safety” certification is enough. I know some of this repeats a bit of what I provided previously, but it’s a good reference paragraph for you if you want to get into the minutiae of the certifications.
What commonly occurs with covers is that you may have a blend of different fibers in the cover - let’s say for simplicity that it’s a cover using 50% cotton and 50% polyester fibers. The cover may be using USDA organic certified cotton for that part of the covering, but the finished cover as a whole would be 50% organic cotton and 50% synthetic material woven together, so the finished cover wouldn’t quality for GOTS certification (see in the link I previously provided about GOTS), as it would have to contain at least 95% certified organic fibers (in our scenario it would only be 50%). So the company could advertise the cover is made with organic cotton (and maybe even weave the term “organic” into the pattern of the cover), but the finished cover wouldn’t be able to be GOTS certified. This may be what you’re seeing in some of the covers you’re considering. The best way to confirm the actual certification would be a detailed conversation with the manufacturer or a knowledgeable retailer where they can explain the certifications, if any, that a product has and to what components those certifications apply.
Phoenix