The issue is not a programming issue.
The problem if the Axoloties are not in sync is that one would generate chunks of samples slightly faster than the other. At some point, there will be too much samples in one direction and too little samples in the other.
Thus, some samples would snap away or a gap would appear, both cases would generate nasty glitches from time to time.
To take account of this drift, some smart software should manage sort of "elastic" buffering. That's not simple and good management and interpolation would eat a lot of CPU.
If hardware sync is possible, there is no more drift and no much less issues.