Why not two 12 volt batteries

They will perform pretty much the same when new but the 6 volt battery's are built with heavier and longer lasting components. They will last years longer than 12V batts.
A lesson I have learned the hard way.

The problem is that as the batteries age, one battery may be weaker than the other. This means that battery will discharge the other battery to the lower level, which prematurely decreases your over all capacity as the batteries age.

The other reason is something I found out the hard way. I used to have 2-12s in parallel, but one of those batteries shorted out. This put a huge load on the other battery which exploded! I was about 15 feet away when it happened. Scared the living daylights out of me. I decided it was not such a good idea after that. You can still do it, but you really need a battery isolator, so that it prevents partial discharge, or that occasional random explosion.

Putting two 12 volt batteries together, you double the amp hours but the volts remain unchanged.
Putting two 6 volt batteries together, you double the volts, but the amp hours remain unchanged.

By using 12 volt batteries, you could easily achiever much greater amp hour capacity than using 6 volt batteries.

My Foretravel came oem with two 12 volt 8D GEL batteries. It now has two 12 volt 8D AGM house batteries. It works for me. It may have been cheaper to go with 6 volt batteries, but I elected to stay with the 12 volt 8D batteries because I would not have to change any wiring, plus if one battery were to die, my coach could still function.

Read The 12 Volt Side of Life. It may help you understand the difference.

Add up the Amp Hours and see if they are Apples to Apples. And it really matters if you boondock.

Indeed! Why not?

Either will work with nearly the same results. This question will generate as much discussion as will a discussion about which toilet paper to use.