It turns out this concept does actually work, just not with the container sizes I originally tested. Since I have discovered that you're not limited to ships of 1K tons in a hangar (which is how I thought it always worked), upping the size of the containers makes everything work much better.
Turns out you're far better off just giving them 3 months of deployment time and having them be civilian, the extra crew requirements are way lower weight/cost than the MSP needed to maintain them. I might redo this with 10K containers, as the larger they are the less wasted mass there is, but it's a tradeoff between carrying capacity and flexibility.
Containers:
Cargo Container class Cargo Ship 4,632 tons 14 Crew 38.7 BP TCS 93 TH 0 EM 0
1 km/s No Armour Shields 0-0 HTK 1 Sensors 0/0/0/0 DCR 0 PPV 0
MSP 0 AFR 926% IFR 12.9% Max Repair 20 MSP
Cargo 4,500
Capitaine de corvette Control Rating 1 BRG
Intended Deployment Time: 3 months
Cryo Container class Cargo Ship 4,965 tons 33 Crew 316.3 BP TCS 99 TH 0 EM 0
1 km/s No Armour Shields 0-0 HTK 12 Sensors 0/0/0/0 DCR 0 PPV 0
MSP 0 AFR 992% IFR 13.8% Max Repair 100 MSP
Cryogenic Berths 19,200
Capitaine de corvette Control Rating 1 BRG
Intended Deployment Time: 3 months
Fuel Container class Cargo Ship 5,000 tons 5 Crew 88.7 BP TCS 100 TH 0 EM 0
1 km/s No Armour Shields 0-0 HTK 8 Sensors 0/0/0/0 DCR 0 PPV 0
MSP 0 AFR 999% IFR 13.9% Max Repair 20 MSP
Capitaine de corvette Control Rating 1 BRG
Intended Deployment Time: 3 months
Fuel Capacity 4,874,000 Litres Range N/A
Supply Container class Cargo Ship 4,998 tons 44 Crew 324.1 BP TCS 100 TH 0 EM 0
1 km/s No Armour Shields 0-0 HTK 21 Sensors 0/0/0/0 DCR 0 PPV 0
MSP 38,540 AFR 1000% IFR 13.9% Max Repair 20 MSP
Capitaine de corvette Control Rating 1 BRG
Intended Deployment Time: 3 months
Troop Container class Cargo Ship 4,975 tons 41 Crew 137.3 BP TCS 99 TH 0 EM 0
1 km/s No Armour Shields 0-0 HTK 10 Sensors 0/0/0/0 DCR 0 PPV 0
MSP 0 AFR 994% IFR 13.8% Max Repair 20 MSP
Troop Capacity 4,800 tons
Capitaine de corvette Control Rating 1 BRG
Intended Deployment Time: 3 months
Ordinance Container class Cargo Ship 4,980 tons 45 Crew 234.3 BP TCS 100 TH 0 EM 0
1 km/s No Armour Shields 0-0 HTK 10 Sensors 0/0/0/0 DCR 0 PPV 0
MSP 0 AFR 995% IFR 13.8% Max Repair 25 MSP
Magazine 800
Capitaine de corvette Control Rating 1 BRG
Intended Deployment Time: 3 months
It's not worthwhile as a wholesale replacement for dedicated Cargo/Colony/Tanker ships because you still lose too much lift capacity to the hangar tax. However, having a modular platform that can cover the less common troop transport, collier and supply ship duties, and be swapped over to standard transport duties when those roles aren't needed is invaluable.
I'm also exploring the possibility of using these modular conveyors as jump tenders for merchant fleets. Storing the drive containers at fleet depots and only breaking them out when there's a need to travel outside the network of jump station. There are some definite limitations on this, since at my current tech level I wouldn't be able to use my modular conveyor design to shuttle my megafreighters around, since the ModCon is based on my standard 100K freighter hull and my megafreighters are 500K., but the idea still has merit.