Only on some bundles. For most of the bundles they don't even do that and the duplicate game simply disappears (unless they've changed their policy in the last few months and I didn't notice yet).

But anyhow, I completely agree with you that the GOG bundles are much better. It's great that the bundle page knows which games I already own on GOG and discounts those games from the price of the bundle. I'm not going to buy every bundle because I'm not interested in every type of game, but for the bundles that do catch my eye I have no problems paying the bundle price even if it means I get a duplicate of a game I own on another service.

If I really like a game, then I probably want the GOG version at some point anyway. It's digital which is an advantage if I already owned the game on disc since I don't have to keep finding my discs anymore. The lack of DRM makes it easier to apply fan-made patches and mods especially compared to the Steam version. And some games are patched to run better on newer versions of Windows plus have a lot of digital extras, which is more than I'd get with either disc or Steam.

So even if I already have the game in another format, the GOG version is usually better and I don't regret re-buying good games on GOG. It would be different if I didn't really like the game that much to begin with since I don't intend to replay it, but the few times that's happened so far I wasn't really interested in the overall bundle anyway.

And on a side note, I think the GOG interface has improved since the last major sale and I find it so much more convenient than Steam's now. I love how it marks off which games I already own when I'm looking down the list. Steam doesn't do that, and it's kind of a pain switching back and forth between my library and the store page to see if I already own certain games on Steam. Steam should do the same thing as GOG where it indicates if you already own a game right on the list of specials.