And thus together—yet apart, (line 54)
Paradoxically, the three brothers share a space, and yet are completely isolated from each other by the chains. Again, notice the use of the dash in the line to emphasize their isolation. Byron sure knew how to use punctuation effectively!
I only stirr'd in this black spot, I only lived, I only drew The accursed breath of dungeon-dew; (lines 212-4)
After the death of his youngest brother, the speaker is completely alone – he's isolated from the rest of humankind.
Lone as a solitary cloud,— (line 294)
The speaker compares himself to a "solitary cloud" in the sky on a sunny day. So not only is he completely alone, but he's out of place – he's a cloud that doesn't belong in the sky, since it's otherwise a sunny day.