With the not so smart charging system in the Transits, alternator voltage can be all over the map depending on what the PCM decides is needed to minimally maintain the battery. The whole concept of smart charging is driven by EPA fuel mileage requirements. The concept is that the less the alternator has to work, the less it's load will be on the engine. As it stands, the smart charging system can correctly charge a single calcium battery or matched dual AGM batteries. It can also handle a third battery in parallel but it must be matched to the other two. I think that in reality you could put as many batteries in parallel as you wish as long as they are all identical and the parallel connecting cables are correctly sized. I probably wouldn't try that without the alternator upgrade.
O.K. well not many of us boondockers are going to want to stack a bunch of group 24 combo (deep cycle/Start) batteries in our van's because at best they are a compromise and not a true deep cycle. They won't last long if we take them down below 40% repeatedly even though they claim they can go to 20%. And, since they are all in parallel the risk of not being able to start the vehicle due to a dead battery is ever present. Heck, it's ever present without any additions.
Instead, we're going to go with some form of long lasting battery and at that point you have to forget about using the vehicle to charge them. Or do you? Redarc and Sterling currently make Battery to Battery chargers that deal specifically with the smart charging problem. Rather than explain them here, go to http://www.sterling-power-usa.com/
and read through their user manuals to decide which unit fits your needs best.
I've had my share of problems with the Smart Charge system on my F-150 and my Transit. After multiple trips to the dealer I developed a phobia about having any of my house systems touching the vehicles system in any way. Apparently, I'm not alone. Sterling has a solution for fully isolated house systems too!
That's my best advice. Take it or leave, I'll still let you borrow my generator to start your van when (not if) you need it.