I doubt something that thin causes any focus issues by the time you’re at F22 or smaller, or that it creates any light leak possibilities.
However, there’s other ways of doing what you’re doing. For example I use sleeves — sold on the auction site, they’re reversible, red or black, so I’ll use that to differentiate eg b&w vs E6. When I need more than two types I simply use painters tape on the outside of the sleeve and write down the film. If its use changes in the future I simply peel it off and write a new one.
I think it’s a good idea to use sleeves of some sort to avoid dust and alike, so at that point, I think it’s better to mark the sleeve with the film type than the holder. That said you’re probably fine, if you’re really worried just take two identical shots with and without a dot and see if you tell a difference. I bet you can’t, unless you bump into the camera between shots
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