as in you create a star cluster within an already existing sector block or a a star cluster off the border of one like Delta Volanis?
I suppose it doesn't matter. In terms of the storyline I'm kicking around, you travel through a portal you discovered on a routine exploration mission which leads you to an unexplored sector of space. Superficially, I imagine it to look like an exploration sector, like Delta Volanis and the others, but there's no reason it has to.
In principle, I think you will be able to do what you're proposing.
Let's say you make the player go to the Toron system. Upon entering the system, they fight with some enemy who warps out after his hull hits 25%. At this point, you could have one of the bridge officers say, "Captain, I've plotted the course of the enemy vessel. It leads to the Devore system."
Obviously, there is no Devore system in game, but you have created one for the player to go to during the mission. In the mission the player jumps to warp, and immediately drops out again, presumably in the Devore star system, designed by you. (In reality, they never left the Toron system, which is where their ship will be in sector space once the mission is completed.)
Essentially, (and this is my opnion) I think every time you create an instance, you're creating a whole new star system. As in, going to the Toron system in my mission will look completely different than going to the Toron system in your mission. Both missions reference the Toron system, but the "look" of the Toron system, the number of planets and the layout is determined by the author of the mission, it is not static like Earth Spacedock, and DS9.
So, you could have the player jump to another "star system" by warping from one instance to another or you could actually force them to fly through sector space to another system to continue the mission.
But will you be able to generate a whole new section of "sector space" to explore, even if it is only an instance...I don't think that will be possible. But there are ways of making the player feel like they've just been nabbed by a wormhole and flung across the galaxy. There may even be a way to have the player spawn at a different point in sector space at the end of the mission to make it appear as though they just re-entered known space on the other side of the galaxy, but that is pure speculation on my part.