It seems like in the Forge they perfected the copy of the human mind. I wonder if that was after William decided to stop the Delos experiment or if the Forge was just withholding the key. Although even Ford said his consciousness had a shelf-life, so maybe there was stil and issue with the human brain in host body, even if the copy is perfect.
As far as the number of time Bernard was created. I assumes with the blue dress conversations were in the Forge, therefore time didn't really matter. The black dress convo was in the real world, she had already made a perfect copy, so she could make another without going through other copies. But what is Bernard? He doesn't seem to be a Arthur copy, he doesn't have his memories. But he is a copy in that he looks and acts like him. Is that immortality? Being able to live on as "yourself" but not with previous memories?
So the MIB sequence at the end if in the far future. And it seems his copy always gets to the Forge elevator. That is that important life changing point in his life. But if its not a simulation, whats going on? Everything looks destroyed down there? On the surface, are there old hosts recreating this whole thing over an over. Who is maintaining them?