Schiit asked me check the Magni with 176.4 kHz tracks, and there is a crackling sound with those as well, so it appears not to be an issue with just on of the two clocks in the DAC but rather a systemic defect in the USB receiver.
I did try the Magni with the Eversolo A8 digital output, which is working fine with my Asgard X with built-in DAC. The A8 digital output did nothing to improve the crackling on the Magni with either 176 or 192 kHz files (all via Roon, although I earlier got the same result using Qobuz directly).
Schiit is paying to have this defective Magni returned and replaced.
So, relevant to the topic here, so far so good with customer support.