I mean ... it sounds like the game you got wasn't exactly as described, though without seeing all the communication it's hard to say. You bought something without even pics, which is kinda crazy to me. You should always feel the need to ask for pics.
But the guy has a point. You bought it, and drilled holes in it.
Now I think those protectors are great. But they're not OEM for the game. I personally couldn't care less about any of that. Non-matching boards? Don't even bother telling me, because I will never check anyways.
I think it's weaselly to sell someone a game without pics knowing about all the issues. So no sympathy for the guy really. But if you're asking straight up does it devalue it? Drilled holes do for some people. I'm not one, but I get why some people would care. Even if I think they're kinda of overly anal.