Sure, an allergy is different than an auto-immune reaction. However, that doesn't change the fact that the body can detect what is applied to the skin. The antibodies are in the blood, and the blood is all throughout the body. So ingestion is not a prerequisite for an auto-immune reaction to gluten.
If a person is having a topical reaction from a particular product, you are correct, that would be an allergy which is a totally different animal than an internal, autoimmune reaction...
Inhaling something like a powdery substance which contains gluten is a no-brainer and doesn't even deserve a comment. I don't think that has anything to do with mascara or eye liner.
As for eyeliner, mascara, etc; let's not forget tear ducts, ears, and nostrils, which are just some of the places where microbes are known to enter the body. Those microbes are a whole lot larger than a gluten molecule. In addition to that, it is a well-known fact that people have a tendency to touch their faces. Just brushing your hair back, handling eyeglasses, or scratching an itch, is all it takes to get a cosmetic product from your face to your hands. From there it can get everywhere - doorknobs, keyboards, computer mice, remote controls, faucet fixtures, drinking glasses, telephones, you name it.
The hands are the most common method for the spread of communicable diseases, and though gluten intolerance and Celiac aren't communicable, gluten certainly can be spread around like germs. Studies have actually shown that a computer keyboard can harbor more germs than a toilet seat. Look here for more on that.
Now, consider if you knew that a cosmetic product had anthrax spores in it. Would you use it, just because you don't intend to consume it or breath it in? After all, anthrax won't burrow through your skin. I'm sure there aren't very many who'd want to even touch the container.
Viruses aren't alive, and neither is gluten, but both can be dangerous. Perhaps one consolation is that gluten doesn't multiply. Come to think of it, viruses have amino acid sequences, and so does the gliadin protein which causes the auto-immune reaction in celiac disease. While I know gluten isn't a bacteria or virus, I think there is good reason to use many of the same cautions.