I believe it's a technical limitation.
I assume it's not one that's particularly hard to overcome I bet it's just way down the list.
My guess is there was some problem that the cap was a quick fix for a problem that's just not been deemed important enough for a better fix.
How onerous is it to replot every 1000 ly, how long does it take you to fly 1000 ly anyway?
the route plotter has already a lot of poblems plotting around the core and other high density star regions. increased jumprange via engineers adds to that. with 2000 or 20 000 ly you might end with a routeplotting time of hours ...