I haul far more crew than the combined minimum for the fleet because I expect to lose crew from combat. +10 crew is insignificant when I have about a dozen warships from frigates to cruisers (and maybe one capital) with higher minimum (and maximum) crew during the time of the game I would consider medium-sized haulers. Late-game, I would move on to bigger haulers like Colossus or bigger (or Revenant).
The built-in Military Subsystems means I can slap Expanded Cargo Holds and one other dock-mod of my choice (Additional Berthing, Auxiliary Fuel Tanks, Efficiency Overhaul, Surveying Equipment, whatever) on it.
You're acting like Militarized Subsystems is mandatory; it isn't.
- Most cruisers have a base burn level of 8 and Augmented Engines are somewhat impractical to fit into most builds without spending story points somewhere. Unmilitarized Buffaloes have a burn level of either 8 or 10 depending on whether or not you took Bulk Transport while militarized Buffaloes have a burn level of 9; unless your cruisers are specifically Eradicators, Falcons, or Furies and you didn't take Bulk Transport, the +1 burn level of Militarized Subsystems is essentially irrelevant.
- If you have "a dozen warships ranging from frigates to cruisers," you're probably talking about 80+ supplies per month just for your warships. Assuming no story points are invested, a Buffalo's supply consumption is between 2.4 and 6.0 supplies per month, and unless you have a lot of Buffaloes the difference between 80 + 2.4n + x and 80 + 6n + x supplies per month, where x is however many supplies per month you're spending on non-Buffalo support ships, isn't going to be large enough to be of material significance.
- If you have "a dozen warships ranging from frigates to cruisers," you're probably talking about enough sensor strength/profile that getting 30 more sensor strength and 60 less sensor profile out of each Buffalo isn't particularly meaningful. Say you have 2 cruisers, 4 destroyers, 6 frigates, and a Phaeton; this gives you either 630 sensor strength and 720 sensor profile or 660 sensor strength and profile before bonuses and penalties are applied; each unmilitarized Buffalo increases sensor strength/profile by 30/120 while each militarized Buffalo increases sensor strength/profile by 60/60, so if we add five Buffaloes to the fleet we're looking at between 780 and 960 sensor strength and between 960 and 1320 sensor profile before applying bonuses and penalties. The differences here aren't nothing, but they're also not especially concerning; neither stealth nor the ability to detect other fleets before they detect your fleet are of particularly great importance except when smuggling or
maybe when trying to do something in particularly dangerous systems before you have a fleet that can deal with whatever's present (although being noticed and then dragging whatever spotted you off to the middle of nowhere before losing them and dashing back to whatever point of interest you were trying to look at tends to work well enough as long as Sustained/Emergency Burn will let you outrun your pursuers).
You can only have two logistical hullmods. If you care about sensor profile, one of them is going to be either Militarized Subsystems or Insulated Engine Assembly. Having MilSub built-in means you can get Expanded Cargo Holds and something else, like ISU for even lower sensor profile or Surveying Equipment for exploration.
How often do you really need hullmod-based sensor profile reduction, Expanded Cargo Holds, and something else while off exploring, especially with a stealth fleet? Phase ships generally have higher-than-average fuel capacity for their size/fuel consumption, being stealthy means you can avoid most fights and so shouldn't particularly need to carry around large quantities of supplies and spare crew to cover combat, most of the stuff you can pick up while out exploring is low-value junk that's barely worth hauling back to the Core even when you were already about to go back, most worlds that don't have ruins on them aren't really worth surveying unless you're being paid to do it because it takes exceptional resources or a hypershunt to do much better than whatever you found in Penelope's Star or Duzahk when you're any significant distance away from the Core (and secondary industries don't actually care about local resources, so unless you can tap a hypershunt an airless rock with high accessibility, such as Dorus in Penelope's Star, is already about as good a location for most of the secondary industries as you'll ever find), hostile things can often be lured away and dodged/outrun even if you can't sneak past them, Pathers can be paid off, and pirates might even be nonhostile due to how often missions that actually benefit from a stealth fleet are offered by pirate-aligned contacts.
Also, any "stealth" fleet worthy of the name is unlikely to get much real value out of stacking both Militarized Subsystems and Insulated Engine Assembly on a little freighter like the Buffalo. You're almost certainly going to have at least a 30% reduction in sensor profile while the transponder is off from phase ships in the fleet, so putting both Militarized Subsystems and Insulated Engine Assembly on a destroyer-scale civilian fleet probably saves you no more than 21 sensor profile (10.5 while darkened) before terrain effects as compared to either Militarized Subsystems or Insulated Engine Assembly alone, and as long as your sensor profile is below about two or three hundred while darkened finding an opportunity to drop off a spysat or sneak up to a colony usually isn't too much trouble even without doing something to bait off the local patrols. A capital- or maybe cruiser-scale civilian ship might be worth both, at least if you're not going to spend a story point on Insulated Engine Assembly, but a destroyer-scale freighter like the Buffalo isn't.
