Even on low gain XLR vs middle gain SE? Hmm. That would be strange to hear that it's more noisy by design.
That's not really fair to say that. However it's understandable that regular people don't understand.
Firstly, you can go to Massdrop 789's page, check the specifications of that. You will see that balanced output is twice as noisy. So by showing this, it's not just A90 that has this property.
Now, if you have access to Douglas Self's small signal book(or doesn't matter if you don't), it's said that balance connection is inherently more noisy than single-ended. While this is not intuitive, it's actually true. If you have balanced to single ended or single ended to balanced conversion, you get even more noise(relatively). Balanced connection however have better rejection to interference.
At this moment, we established that this is common and not a strange phenomenon.
Then, in comparison, A90's balanced output, even though is relatively more noisy than single-ended output, has much less noise of single ended output on many amplifiers even compared with 789. 0.6uV vs 1.2uV. Single ended output of A90 is just lower at 0.2uV. Probably the lowest on the market, at least to my knowledge.
Lastly, does it matter. Maybe yes maybe no. Most of the headphones aren't noisy with over 4uV noise. Most sensitive IEMs can produce audible noise with 0.8uV noise. So it really depends. For the user, just try it. Pretty simple.