Not sure we have the full story on the MiB/Smoky connection. Note that they are not ever shown quite localized: i.e. Locke vanishes inside the chamber and then Smoky floods into the chamber from the outside. Smoky leaves via the door and then Locke reappears inside the chamber, behind Ben. They may be a connected entity, but I’m not sure the rules/personality are the same.
Other oddities: Smoky has always struck me as not being quite of human intelligence, whereas MiB is extremely cunning. Surely MiB wouldn’t be fooled by people running into trees and if it really cared about catching the people its chased throughout the series, wouldn’t have been so easily deterred or put off. We know that the Others can summon Smoky and sort of have it do their bidding, which strikes me as odd for the MiB. Perhaps parts of him are trapped and other aspects of him can reach out and touch the world in certain ways.
As to what happened after the Incident: my theory is that if the bomb truly destroyed the Swan, then the plane never crashed. But if it never crashed, then the Losties never went back in time. And then all sorts of stuff in the past is different, leading to the Island sinking, but NOT from Jughead! From something else. Hence, LA X.
But I bet that the LA X timeline will culminate in explaining the origins of original timeline: i.e. LA X storyline will be about moving all the pieces into place to make the Lostees crash/have linked destinies in the first place (i.e. Jacob or whomever Islandy is still operating in the LA X timeline will enlist them all to work and fight whatever great evil came of the Island being sunk, and the ultimate solution will be to prevent whatever caused the Island to sinking, thus allowing the Swan to be built, crashing the plane, etc.).
So, in that sense, Juliet’s bomb both works AND fails, the timelines both existing AND leading into each other.