The key is connecting the balance taps so the 2 lipos are balanced together as a 4S lipo. There's no reason it won't work if you balance them together as single batt. The reason its not recommended is the wiring has got to be right for the balance taps.

Airplane guys do this a lot - RCGroups' batteries and charger forums is a good reference. You can also PM BrianG, mod on RCMonster forums about doing this - he's a mod on another site (can't remember) and I've read some of his discussion on how to wire the balance taps.

The easy way is a pr of networked 0610i chargers.