It does, but it doesn't always.

For example - if I have a star system that's in Delta Volanis Star Cluster, it wouldn't make sense to, say, fly to Vulcan.

In that case, just leaving out of Sol would be more practical.

Correct, using what I said about cities, I wouldn't use Buffalo to describe how to get to Rye. It would be nice if cluster borders could be doors though.