On these DLCs, from what I understand, the retailers are demanding them, which in turn makes the publishers demand them. It's like the DRM, they didn't want it in the first place but that's the way the business works these days if you are making a big release.
By doing what they did, just as removing the DRM, it was their attempt to level the playing field and make sure everyone has the same game. Bioware, by the way, has never done this. Even with Dragon Age Origins there are still some pre-order bonus DLCs they did not bother to include with the "Ultimate Edition" and have seen those selling for quite a bit on Ebay.
CD Projekt didn't want people to get caught up in the DLC craziness so they initially announced you would only be able to use one DLC and would have to choose, but many people complained and the Collector's Edition people felt cheated they would get the Roche suit but not the vendor DLC so they relented and removed that restriction prior to release.
I think they are just trying to make everyone happy as best they can given a situation where in some situations they are forced to release under circumstanced they would have preferred otherwise. They feel the best solution at this point is to just make it so that everyone's game is the same, a level playing field.
Personally, I wish the stores would stick to physical bonuses, like the exclusive Witcher comic book Gamestop shipped with for instance. The retailers feel otherwise though and want the exclusive DLCs. They are in many cases unbalancing. I played through DA:O my first time with the Ultimate version and I regretted using the Feast Day Gifts that instantly made everyone my BFF. On the other hand, I as the player need to exercise better self control and not use things I know are overpowered or will ruin aspects of the game for me.
A mod to yank these items back out should be easy enough to do, but I'm also afraid to mess with mods given that the game refused to patch this time for anyone who used them.