What is there to square? Those mod don't get taken almost ever because of limited OP or specifically limited SP, the only ships with the OP can't take them because of the arbitrary limit. Those SP shouldn't have to be spent on secondary fleet bonuses, which are frankly minor, when the combat ships need them more for survival and fighting power.
The logistics limit exists for no reason. There is no balance argument that can be made for it continuing to enforce it.
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.
The number of logistic hullmods you can place your logistics train directly affects how large that logistics portion of the fleet needs to be (translating potentially into more slots for combat ships out of the 30 soft cap), or alternatively increasing profits for a lower investment and running cost, as well as those 3 campaign map statistics which determine how often you have to engage in fights you don't want.
You can keep your fleet's profile small and burn at 10 by using 26 hounds for 1950 cargo space, limiting you to 4 combat ships, or you can use an Atlas for 2000 cargo space, at the cost of dropping to burn 6 with a 150 or more increase in the fleet profile, but allowing 29 other combat ships. That is an extreme, but real potential comparison of fleet setups. Logistics mods then directly affect those numbers.
While I can see being what the ideal balance point being hard to pin down quantitatively, I do see there is a balance to at least be considered. If a 15 Atlas, 15 Prometheus fleet was as fast and hard to detect as an all phase frigate fleet, then I would agree the logistics hull mod limit exists for no reason. But there is a multidimensional continuum of campaign stats that logistics hull mods move ships in different directions on, and by limiting hull mods, you are restricting how far you can move from the initial starting point, which looks like a balance consideration to me. In the same way that OP limits combat ship stats all going up to the max as well.