A thought came to me, reading all the theories about the reality of the show being distorted.
One of the ideas has been that the events in the series are on a loop, but they might play out differently, in different timelines/universes/dreams...
I'm not saying I strongly support these ideas, but if so, then such an interpretation might "rescue" the European pilot ending as "just as real" as the ending of the proper show? This because of how free to interpretations the finale has been.
There are some parallels to the way BOB was beaten in this finale and the way he was simply shot in that pilot episode. Also, as has been noted, the Great Northern basement scene resembled the setting BOB was in the hospital basement (only a glimpse of it was shown in the series).
One could think the "boiler room basement/door in the basement" becomes established as a fixed point in the mythology, almost comparable to the "room above the convenience store", something that remains through all interpretations/ timelines/ dreams/ realities /fan theories, despite where it might be located.
Then the European Pilot ending would be one blunt, short variant of how the events pan out, just as valid as anything else.
Playing on a loop so the Black Lodge residents can live on the pain & sorrow of Twin Peaks residents?
The infinite loop is certainly seen during the show. Perhaps their lives are replayed slightly differently each time? A similar idea was used in The Matrix.
Could this be why Paige screams when she sees the Palmer house as she recognises it from one of her previous incarnations?
No doubt anyone's idea is as valid as another. Everything is ambiguous and open to interpretation after Episodes 17 & 18. Nothing is grounded at all anymore, the whole mythology is in quicksand. What if Sarah Palmer was "the dreamer" of the original series? She dreams up "Bob" somewhere along the way because she can't accept her husband is a pedophile rapist murderer? Who knows..