This is correct, the only downside to charging both at the same time is each battery is charged at a slower right, taking longer, due to less current to each battery. The convenience of dual charging is plugging them in at the same time. Then after you're done with dinner both batteries are charged, ready to store away for the next flight. A LiPo power supply will only put out what it's rated at, no more. It doesn't know if it's going to one battery or two, when charge two depleted batteries, it's simply putting out it's full power, based on the sensed voltage level, which is sensed by the battery circuitry in the RC, and in the intelligent flight battery, the so-called smarts. The flight battery has more smarts than the RC battery, since flight batteries are more important and work much harder, and cycled more times.
It's important to know the flight batteries, if accidentally left on overnight they will automatically turn off when they reach 3.0V to protect the battery. If the RC battery is left on accidentally the RC will beep at you after a while, but the battery will continue discharge. I don't think the RC will automatically shuts off at 3.0V/cell like the flight batteries, which may be why some people report problems with batteries failing in the RC. I'm wondering how many of those that report RC battery problems had accidentally left the RC on long enough to run the battery totally dead.
It's also interesting to know, there are a lot of reports of brand new flight batteries that won't take a charge. The batteries are actually discharge to a state where the smarts won't allow the battery to charge. If you take the battery apart (which is a pain) and you physically bypass the smarts and put a charge directly to the battery, the battery cells will charge up. If you put a just a short charge into the battery, say 20 minute worth, you can then reassemble the battery and it will charge like normal and usually have a long and health life. There is a guy on Ebay that sells new batteries like this that won't take a charge for like $35/ea. If you a have the skill set and patience to disassemble the battery and perform a "manual charge" on the cells, you can get some bargain deals on used/new batteries. I think the seller even provides YT video to show the "jump start" process, but I may be wrong.