I think it could be. If you want to set up hyperwarp as a thing that provides immense convenience/mobility options with significant costs/downsides it could be quite a handy option. Personally I find that fuel starts to become a non-issue towards endgame, and the ability to instantly jump my lumbering megafleet damn near anywhere in a system to be a very powerful tool. An in-system fuel cost could make it more of a tactical choice than a default mode of travel.
Making the fuel cost scale with burn level rather than distance could make it work better with adjustments to the 'distance per burn level' and 'fuel consumption mult' variables as well, using the fleet's fuel/LY rating and leveraging that as part of the cost formula along with the burn level as a surrogate for distance traveled, altered by fuel mult and a separate in-system mult value. Just an idea, I have no idea how difficult it would be to actually implement.
Thematically it also kinda makes sense, as I imagine the jump is like a quick 'skip' across some surface/dimension/brane of hyperspace and thus needs fuel just like travelling through hyperspace proper. But that's just reverse-fluff for balancing mechanics
Personally I adjusted it to have around 1/5th the distance/burn level, 2x fuel cost, 1.5x CR cost, halved the interference effect/sensor increase and put the mission time multi at 1, again since I like the idea of it being a more tactical maneuver than a fast travel ability. I still find it a very useful tool, as does the AI
edit: kinda been playing around with the settings, looks like with the settings described above (+ a 1.5x interdict range interference, ~1.5k sensor profile increase and 1.5x fuel cost) it works as both a costly fast travel method (about 2x faster than normal at 20 burn) and a cool tactical ability. An in-system fuel cost I think would really give it that useful-but-risky/costly feeling. It feels like a dangerous high level navigation thing that crappy sector ships are just not designed or equipped to do constantly. Also agree with SafariJohn about the transponder-off identification not making much sense. I think that patrols detecting a huge signal spike from a t-off warping fleet should set off enough alarm bells without that fleet being immediately identified. But maybe it also makes sense given the huge distance it normally allows you to travel. Perhaps that could also be a settings option?
edit 2: sorry for all the words.