The fanciest of moustaches
An Unlikely Duo provides some implications that the Mysterious Stranger is Sepulchure's master.
We have the Stranger's appearance itself. Conveniently, it is immediately following Drakath's death. Such timing would require one to have some way of knowing that the battle had ended with Drakath's death at that exact moment, yet the only people present are Sepulchure and the PC... and Sepulchure's weapon, which we know is tied very closely with Sepulchure's master. So, three people should be aware of Drakath's death at the exact instant Drakath dies: the PC, Sepulchure, and Sepulchure's master. The one who appears closely thereafter is the Mysterious Stranger. This could be coincidence, but it implies that the Stranger is, in fact, the master.
The next bit that implies the Stranger is the master is its "You were a puppet" line. The context here is more important than the line itself.
Sepulchure: But... but I am a creature of the darkness! I was promised this world!
???: You were a puppet.
The Stranger seems to be acutely aware of the promise to Sepulchure. In fact, its statement even seems to imply that it was the Stranger who made the promise. The promise was the strings to which the puppet Sepulchure danced. It was nothing but a lie, a means to manipulate Sepulchure, and the Stranger knows this. How else could the Stranger know this, then, if not Sepulchure's master?
So yes, I'll agree that it was never outright confirmed. However, it's certainly implied that the master is the Stranger.
The Stranger in MQ is... a slightly different bag of fish. He seems to function primarily as the Stranger in DF does, and indeed very likely is one and the same, given the closeness between DF and MQ. It is very likely that he is simply biding his time for a monumental event to occur, such as what happened in DF with Dragon Drakath. As for what he does with the souls, well, I imagine that the souls, being those of ghosts, are primarily Darkness in nature, so he likely assimilates them in order to gain power a bit faster.
I do look forward to seeing what the Stranger will do in AQ, now that he's been "invited" in. With Erebus's downfall came a vacuum of power, one that the Stranger we saw (whether or not it actually is DF's remains to be seen, as it may simply be an alternative timeline that has run very similarly to DF) and may yet take advantage of. I believe that many questions regarding the Stranger will be answered then.
As for the Stranger's capability to sense other Strangers, it is my theory that this has to deal with the primordial nature of the Stranger. If it truly was present at the creation of Lore, if not the universe itself, then it was almost certainly an existance before the timelines had ever separated. Due to the Stranger's nature, it seems plausible that the timeline split would not have the same effects on the Stranger as on others and that it would maintain an awareness of its other selves as the timelines developed. Though it's quite the stretch of a theory, it's the only reasoning I can come up with that strikes me as feasible. Truth be told, I'm not sure why it would be or how exactly it would work, but it's the only thing I've got in terms of theorizing.