Currently at the highest difficulty enemies in the 90-100k range can appear in amateur zones. Some of these pose distinctive challenges where the only affordable general solution seems to be to move to a missile kite as there is not yet enough money to build a variety of ships or a functional generalist. When missiles inevitably get nerfed again or PD buffed this difficulty may become excessively luck based in not meeting certain enemies in your second or possibly third systems. Once you have a good missile kite going there's no incentive to not just pile on more of the same ship as you can afford them, which tends to result in degenerate gameplay.
On the other hand the late game difficulty is set only by galaxy size, which can limit your endgame budget in a meaningful way on the smallest setting. Vanguard zones don't really get any harder because there are no out of depth ships.
I'd suggest rather than scaling what ships can appear in which zones by difficulty, scale what can appear in fleets. At higher difficulties perhaps an in-depth enemy could appear with smaller escorts, or even groups of ships that would each individually be in depth. This would let the difficulty settings impact the late game more while not allowing second system game game breakers.
Another option is to make difficulty effect NPC component stats, probably HP for the smoothest scaling. Fleets may not be more dangerous than their most dangerous member against some design philosophies.