The whole 'combined functionality' is more that you're working on the assumption that there will be gas giants with atmospheric Sorium in every system that you need a repair/refit base; fuel harvester modules represent a nontrivial amount of tonnage, not to mention that a combination base will both require more specific conditions to be efficient as well as a larger shipyard to produce.
Also note that a maintenance facility requires 75 tons each of Duranium and Neutronium, giving it a resource:functionality ratio of approximately 1.14 tons of support capacity per ton of mineral. A maintenance module requires 100 tons of Neutronium, giving it a ratio of 2 tons of support capacity per ton of mineral, true, but it must also be noted that:
1. Maintenance facilities can be constructed with industry, and thus don't tie up shipyards.
2. Half of the cost of MFs is represented by Duranium, one of the most widely available minerals. The greater Neutronium cost of the modules during a crunch can damage critical production, as it is used in power plants, magazines, shipyards, ground units, and GFTFs.
3. You also have the mineral cost of the rest of the support base. Since you're apparently going with a self-propelled design, I'll also account for engines and extra fuel in this. I threw together an optimum design using mid-level (Internal Confinement Drive level) tech for a self-propelled survey vessel support base:
Collingwood class Maintenance Base 31,050 tons 800 Crew 1620 BP TCS 621 TH 750 EM 0
1207 km/s Armour 1-88 Shields 0-0 Sensors 18/18/0/0 Damage Control Rating 1 PPV 0
MSP 33 Max Repair 200 MSP
Maintenance Modules: 5 module(s) capable of supporting ships of 1000 tons
Internal Confinement Fusion Drive E0.4 (3) Power 250 Fuel Use 4% Signature 250 Armour 0 Exp 1%
Fuel Capacity 630,000 Litres Range 912.5 billion km (8750 days at full power)
CIWS-250 (2x8) Range 1000 km TS: 25000 km/s ROF 5 Base 50% To Hit
Thermal Sensor TH1-18 (1) Sensitivity 18 Detect Sig Strength 1000: 18m km
EM Detection Sensor EM1-18 (1) Sensitivity 18 Detect Sig Strength 1000: 18m km
That's fairly bare-bones if you're looking for it to not be useless and die as soon as hostiles find it. The cost is 1620BP and 1620 tons of minerals for 1000 tons of support capacity. The equivalent in MFs would be 750 CP and 750 tons of minerals. So while the base maintenance module is more efficient than the facility, facilities don't require much support beyond a bit of infrastructure and a few colonists, two of the cheapest resources around. Facilities are also less painful to have overrun, not least because they're not always going to be targeted by hostile ships. Also notable is that MFs become progressively more efficient in comparison to bases as the size of ship they support rises; once you're talking about proper cap ships, bases are going to be so large that you'll need a pretty damned impressive shipyard just to build them, all other costs aside.
Personally, I tend to go for tug-moved structures for my maintenance bases and fuel harvesters to, but even then I rarely use bases when it isn't absolutely necessary. Of course if you're already building space stations to house colonists, that's always an opportune time to tack on things like maintenance modules. Situations like that aside, however, you'll rarely have survey ships that both a) manage to survive long enough to need overhauls and b) make it far out enough that one of your colonies isn't practical.
Still, there are as many design philosophies as there are players, neh?