They're the same faction with the same exact goal, except each with a different Emperor. Am I correct, or am I not seeing this correctly?
Besides Hideyoshi being dead, it's sort of the same thing.
Most of FL stuff is based on Earth history. Exiles have taken this a step farther and is based on Sirius history!
Not exactly. The Exiles (/Samura backed dynasty) is a more conservative, isolationist group. The Blood Dragons (/Hideyoshi dynasty) is more open towards foreign cultures. They are both imperial groups, though.
While BDs are actually being not Imperial group. Hideyoshi was a shogun, not the emperor.