I'm gonna idiot-check you (boy is there ever a phrase that doesn't translate well...) on the problem with all the weird edge cases ur dealing with RE: permanent skills to prevent respecc cheesing. Why not just allow the cheese but make it cost? You
could make respeccing (after you leave the skills menu) lose you the elite tier of permanent skills* you abandoned, then in order to get that elite tier back you have to spend another story point to re-elite it. Now, every time you cheese the respecc it costs you 2 story points; the game doesn't take away the things you got from the cheese, just the ability to keep getting them.
So if you respecc cheese an elite tier that gives a hullmod, the hullmod is still on the ships you put it on, but you can't put it on any other ships after that without spending another skill point & story point to reacquire that skill & its elite tier (or 2 story points to respecc & upgrade).
Or, flux vents/capacitors increase; let players respecc cheese the elite skill to unlock the increase to capacity, stick extra on the ships they want/need it on then respecc off of it. Any ships they acquire after that are stuck in normal capacity unless they re-spend the resources reacquiring it. You could even make salvaging ships have a chance to/always set their vents/capacitors down to 0 or at least back down to the cap if it's over, so that losing a ship becomes a threat when you've spent 2 story points getting its reactor past spec.
In fact, it seems like the only thing you'd need to make any permanent elite skill work fine while allowing the respecc cheese is a way -- or reason, to lose the thing you got from it. To whit, the only thing I can think of that doesn't fit that criteria rn is officers, since there's no way or reason** to lose them after u get ones u want.
** bbbbbbbbuuuuuuuuut, i happen to recall some individual who sounded pretty smart and handsome make a post suggesting the ability to sell(?) fully trained officers for story points. *eyebrows waggle suggestively*
* permanent skills would need to be renamed. Impermanent skills? Temporary skills? Transient skills?
This kind of skill?
edit: also if you feel player controlled redacted is too much you could balance neural integrator a little more, not by making it less effective or cost more than it does, but by also making it guarantee that the ship is lost for good if it dies in battle. So you do get to play with the super special fun toy, but you better not drop it or daddy alex will take it away. Which would make it, not only fun, but also more tense than piloting a normal ship. (also if you were me, and thank god you arent, id make installing neural integrator toggle ironman mode on until the ship it's on has been lost. just as a small act of cruelty. call it a mysterious act of the AI god's love. even when you think you've tamed it it makes you suffer, just to prove your dedication to it)