Do ships get progressively harder in rebel-controlled nodes in the same Sector?
I highly doubt that the Elite Fighters get any more difficult if you hang around in a sector, jumping between rebel-controlled beacons. Difficulty of enemy ships is usually based on the difficulty setting, and what sector you're in. There's no reward for defeating the ships at Rebel-Controlled beacons other than 1 fuel anyway, so there's not much point deliberately hanging around.
Hope this helps.