Hm, it seems that page does have the answer:
Q: I have some interrupt timing sensitive code that I have always wanted to run while also driving NeoPixels. Are you saying this might be possible?
A: No problem! As long as you can keep your interrupt service shorter than ~5us, you can leave interrupts on almost all the time while driving your NeoPixels. The only place where you need to turn them off is during the very brief moment when sending a 0-bit pulse to make sure that it stays below the maximum T0H length. If you add the following code to protect the sending of the 0-bit in sendBit() …
I'm not certain that my audio interrupt is less than 5us, but I did calculate there's 45us between samples, so... maybe it will work?