The reason why they dont put DLC on the same map as the base game is mostly due to limitations in how games works.
Its an often stated rule that the base game can effect DLC, but the DLC cant effect the base game. Hence why you can tell people like Wernher and Graham that you know of the Pitt from some guy in the citadel, and that you killed Caesar, but you cant tell Kodiak that you went to The Pitt, or tell Caesar that you killed Graham.
Its basically impossible for them to get all the people they used for all the VAs in the base game to record new lines regarding DLC stuff, so they put DLC stuff on its own maps with its own VAs. Trying to put it on the same map as the base game only results in a Dawngaurd situation where all the new lines for the hold guards were OBVIOUSLY recorded by an entirely different guy then who did the VA work in the base game, making them sound off.
There are also problems with leveled lists. If Dawnguard added new items to say... bandit's leveled lists, then Dragbonron added the stuff it did to bandit leveled lists, the Dragonborn leveled lists would overwrite the Dawnguard ones, making the items from Dawnguard not show up since its edits would get overwritten.
Skyrim actually had some problems like this, which forced Arthmoor and the team to make a combined unofficial patch to fix them, since its impossible to fix with individual unofficial patches for each DLC.