I am perhaps misinterpreting your statement, so please correct me, but it sounds like to me that you're implying there are no balance considerations for the campaign and navigation layer. I'm pretty sure a giant profile, low sensor range, and low burn fleet (a fleet with all civilian tags and no mitigating hull mods for example), is going to be found and caught by hostile fleets more often than a small profile, high sensor range, high burn fleet. Especially if neither has transverse jump.
I'm saying that there is already a self imposed penalty connected to Campaign vs Combat hull mods, the OP cost.
The Campaign hull mods are inferior to combat by such are margin that unlocking the logistics limit would have minimal impact on the lions share of ship/fleet builds. Because those OP are already needed elsewhere, combat related specifically.
All the logistics limit does is prevent weird/exotic fleet builds like a crazy stealth fleet or super high detection range fleets that use them to avoid combat. To do that now you are forced to use SP, because of the limit. Even if you were willing to sacrifice the fighting power for it. The logistics limit is preventing interesting fleet builds that focus less on combat by forcing the use of the players most valuable resource SP to achieve them.
SP aren't unlimited, I don't care if they are in theory, they massively slow down late game and when you start wanting to use them for colonies you will be able to blow 20 SP with 3-4 clicks. SP are too important to spend on minor campaign upgrades. Early game it's raining SP, you spend them like you are drunk and more pour down. Late game you wish you hadn't been so wasteful.
So why does the logistics hull mod limit need to exist at all? Why does the Atlas in the first post need to waste 2 SP for such minor Campaign bonuses? I have never heard a good answer. That Atlas isn't overpowered because of those 2 SP, it's a really good support ship mind you, but I can sure a hell make a fighting ship overpowered with 2 SP.