Generally, 12 volt batteries in parallel will have issues if they are different ages and sizes and manufacture, but only really if they are left in parallel while being discharged.
2 12 volt batteries that are equal in the above factors and are sitting next to each other and wired in a balanced manner will not suffer effects of one battery taking more of the load or charging than the other.
When you have one battery in the engine compartment, then another 24 feet away(Full circuit length) with an isolator inbetween, then yes the charge/ discharge rates will be very unequal, and one battery will die before the other.
With 2 six volts, they are going to be next to each other, and there is no way to wire them in an unbalanced manner. Think of 2 six volts batteries as just a 12 volt battery that comes in 2 pieces. All you need to do is hook a wire from the negative of one to the positive of the other.
Wiring 12 volts in a balanced manner means taking the ground off one battery and the hot off the other, instead of the ground and hot off the same battery. Imbalance becomes more noticeable with more than 2 batteries, with too thin of interconnecting wires, and higher loads, or charging amps. Generally with just 2 equal size/make/age/manufacture batteries in parallel, right next to each other, the difference would be negligible but indeed measurable for the over analytical.
The real issue with six volts is their height, and the fact that if one does develop a shorted cell, then you have a 10.5 volt battery, or just a 6 volt when removed. Lose 1 of 2 12 volt batteries, and you still have 12 volts to power your accessories, just half the capacity or approximately so depending on the load and the Peukert effect.
The issue with 12 volt batteries is that getting a true deep cycle battery is much more difficult as so many that list "deep cycle" also list marine, trolling, rv on them, which makes them a dual purpose battery, which is just a starting battery slightly more tolerant of deeper discharges. A true deep cycle 12 volt battery has much different construction.
With 6 volt golf cart batteries you are getting a battery designed to be deeply cycled. They do not make 6 volt golf cart sized starting batteries, and this, IMO, is why many people say they get better service out of them.