Militarized subsystems I find is an early game compromise hullmod that you have from the beginning of the game. It is quite good at the stage of the game where you have less than 240 DP worth of ships in total, at which point the skill fall off doesn't even happen. It's +1 speed, reduced sensor signature in a single hullmod, allowing for another logistics hullmod without penalty, where as +2 burn from Augmented Drive Field and Insulated Engines take two, and even if you use s-mods, expanded cargo holds or auxilliary fuel tanks still adds some additional expense.
It definitely falls off in use late game, but the whole concept, militarizing civilian ships, is by its nature a "make do with what you have" philosophy. Late game you aren't making do; you're specializing your fleet. I think it is fine to have such hullmods useful early game, and as the game transitions, for them to stop being used.
As for Revenants, I think they're perfectly fine late game transports for combat fleets - if you can acquire them. They're not as efficient as an Atlas or Prometheus in terms of raw cargo or fuel capacity per credit, but on the other hand, they're not capitals, which does weird things to your fleet's campaign maneuverability and efficiency traversing deep hyperspace and the like, not to mention ballooning your sensor profile if you're not already stacking 5 combat capitals. I certainly prefer them in "light weight" high tech fleets. High DP cost but small physically ships like Hyperions, Scarabs, and so on maybe with a single fast capital leading the pack. A low tech Onslaught/Legion heavy fleet likely would just grab a couple Prometheus though. Might still slap an s-mod on them though for either +2 burn or insulated engines.
Your typical late game logistics solution options are basically:
Atlas (Pro: 2000 cargo/400 fuel, Con:Civilian, 50 crew, 10 supplies/month, 6 fuel/ly, 6 burn base)
Prometheus (Pro: 200 cargo/3000 fuel, Con: Civilian, 50 crew, 10 supplies/month, 6 fuel/ly, 6 burn base)
Colossus (Pro: 900 cargo/120 fuel, Con: Civilian, 40 crew, 6 supplies/month, 4 fuel/ly, 7 burn base)
Phaeton (Pro: 20 cargo/800 fuel, Con: Civilian, 10 crew, 4 supplies/month, 2 fuel/ly, 8 burn base)
Revenant (Pro: 600 cargo/900 fuel, phase field, Con: 30 crew, 15 supplies/month, 3 fuel/ly, 8 burn base)
Let us assume no story points spent s-mods, and just slap on expanded cargo hold or auxiliary fuel tanks along with insulated engines to get the sensor signature down. Revenant just has both cargo and fuel mods (and still will tend to have smaller signature and full cruiser sensor benefit).
Colossus + Phaeton: 1190 cargo and 1160 fuel
50 crew (500 credits/month), 15 supplies/month (1500 credits), 6 fuel/ly (150 credits per light year)
Revenant: 780 cargo, 1170 fuel
30 crew (300 credits/month), 15 supplies/month (1500 credits), 3 fuel/ly (75 credits per light year)
You're trading off about 400 units of cargo for one fewer logistics ship and slightly longer fuel endurance (30 light year trip from the core out and back is 180 fuel difference, so 1160-360=800 fuel for other ships vs 1170-180 = 990 fuel for other ships. Plus the advantages of a smaller fleet profile from phase field.
The Atlas and Prometheus are more efficient, however at the cost of adding capital logistics to your fleet (i.e. base 6 burn, which either means Bulk transport late game, taking a hit to sensor profile, and whatever the behinds the scene calculation for terrain and campaign maneuverability there is).
Atlas + Prometheus: 2800 cargo, 4300 fuel
100 crew (1,000 credits/month), 30 supplies/month (3000 credits), 12 fuel/ly (300 credits per light year)
3x Revenant: 2340 cargo, 3510 fuel
90 crew (900 credits/month), 45 supplies/month (4500 credits), 9 fuel/ly (225 credits per light year)
For a 2 month run (15 days out, 30 days exploring/hunting bounties/etc, 15 days back), going out 30 light years and coming back 30 light years, most of the expense is in the fuel.
18,000 credits in fuel versus 6000 credits in supplies and 2000 credits in salaries for the capitals (or about 9.2 credits per cargo, and can handle a 59.7 fuel/ly fleet).
13,500 credits in fuel versus 9000 credits in supplies and 1800 credits in salaries for the Revenants (or about 10.4 credits per cargo, and can handle a 49.5 fuel/ly fleet).
Although, at the point of the game where I'm considering between capital logistics and Revenants, I really don't care about a few thousand credits here and there, and just tend to grab the Revenants for the better sensor stats. I'll take a hit of 10% to my logistics credit costs for those sensor stats in an iron man game.