You're right. It doesn't explain how it goes with X1 (or X1A). They couldn't have the original SOC DAC inside. Even if they did (seeing they use the snapdragon SOC too), they must have hard-wired the routing to the sabre DACs.
If you read the product page they insinuate that they achieve true balanced mode via the dual amps and DACs. The other dual DAC players like a&k use a balanced output for that same reason.
EDIT: If you read what david previously posted, Onkyo USA stated that Both DAC's and BOTH amps are used for BOTH 3.5 and 2.5 balanced IN the onkyo music player.
However with third party apps, though it has NOT been tested, they are assuming it goes through ONE dac and BOTH Amplifiers. BOTH left and right channels go through each DAC and AMP together in the music amp. 3rd party apps would put BOTH left and right through BOTH amps, but only ONE DAC.
^Honestly, unless we pester Onkyo for actual data, we aren't going to get much farther than this. IMO, we need to let Onkyo know that we want more information on the X1A. Also, if a company like FiiO can test 3rd party compatibility with DACs, then Onkyo should have no problem.
It's a bit ironic, the reason why fiiO's software is having problems is because the company they hired to implement android 5.1 backed out of their contract, and demanded more money, which FiiO couldn't afford. So FiiO had to implement android themselves, hence all the hiccups they've had along the way. However even that fact that I'm able to tell you this shows their customer support is very close with their customers and is very honest. You always know what they're working on, what updates to expect, etc.
Onkyo has all the resources and money, so obviously android is very well implemented, and the quality of the device is superb. However we sit here, 800 pages in, and we still have questions about how the device works... this is ridiculous. Don't get me wrong, I love my X1A, much much more than the X7 I used to own. But we need to let Onkyo know something's gotta change with this type of support. We, as their consumers, shouldn't be ok with this.