Hmm - I don't think the penalties from civgrade are nearly that bad. Especially if it's a smaller ship in a larger fleet, you often don't need +1 burn and the sensor penalties don't matter. Alternatively, you can put Augmented Drive Field on larger ships to get its burn up to par, and Efficiency Overhaul or a capacity-expander may be worth more that Militarized Subsystems, depending on how you feel about the sensor penalty. Or you might go for ADF and MS for maximum burn. I'm really not seeing it as being that clear-cut! Especially considering that MS increases the cost of running the ship.
I don't think it's really an alternative to use augmented drive field or insulated engine assembly to cancel the penalties of civilian hull because those both also cost a logistic hull mod slot. It's the same issue where you have to lose logistics slots to cancel the penalties.
My logistic ships are almost always the largest ships in my fleet because otherwise I am wasting fleet slots on logistic ships that don't contribute to combat (or at least much less) and don't improve my logistic capability when compared to the larger ships. Like the buffalo has less cargo per supply cost and cargo per fuel cost and requires more fleet slots for the same cargo (with or without expanded cargo holds) than the colossus, so why would I use buffalos? The only reason for using smaller logistics ships is burn level and sensor profile. If I can tolerate a worse sensor profile and burn speed from not having MS on a small ship, then I will just use bigger logistics ships with MS (and probably augmented drive field) which perform better in almost every other metric. Basically, I don't think using smaller civilian ships in a larger fleet makes a lot of sense when the bigger civilian ships are just better overall for the fleet.
Maybe this is more an argument for buffs for small logistic ships, but I think the fleet cap issue will always still push the player towards big logistics ships.
Also the effect of those decisions on smaller ships matter a lot less. By the time that my fleet is big enough where MS on a shepherd or buffalo wouldn't matter, my running costs have increase enough that using something else doesn't matter either. My 300 supply per month fleet of cruisers couldn't care less about the .6 supply per month savings of putting efficiency overhaul on a shepherd.
Maybe I just value sensor profile and burn speed too highly, but it really never seems like an interesting decision to me based on the logical points to transition to larger supply ships.
