Clarify this: do you mean you have to pay the "holding fee" on everything once you get a Class 3 or what? A very good friend of mine has AP for his .223 and .308, neither of which have any "holding fee" associated with them. Yes I'm sure there was a sales tax applied at sale, and possibly some federal tax because it's ammo, but I'm not sure about the latter because I've never bought any ammo. I just shoot his :)
Also I don't see this "holding fee" happening for things you can buy online, like ammo. My friend gets all his ammo from online, it comes in nice metal tins covered in Russian / Bulgarian whatever writing. He also has what I'm guessing you mean by high capacity (30 round magazines) and there was no fee.