We speak to USB via a driver, and have no direct access to USB commands at the level he is describing. Only the driver can send those commands.
But…even if we could, we shouldn’t. It is the responsibility of the USB interface chip + the DAC chip together to manage mute states in order to keep things quiet during transitions. For us to do it would be a hack–ultimately if a DAC is making noises on transitions, it’s always the DAC’s fault(*).
In most DACs, the interface chip tells the DAC chip to mute shortly before performing a transition, and then to unmute shortly after. Many DAC chips have mute implementations that can perform a short fade in/out on mute/unmute to allow for clean transitions on S/PDIF sources, too. This is just an expected task when integrating a USB interface with a DAC chip inside of a DAC.
Every once in a great while, we have run into a product that manages this detail poorly. We usually take up the issue with the manufacturer, and they either decide to fix it via an update, or if that’s not possible, they at least resolve to avoid the issue on future products.
We have two Amanero-based DACs here that make clean transitions on their own, with no “help” from the player–so we know it’s possible.
(*) One exception to this that I’m aware of: There was a version of the Linux kernel that sent a 00000000 PCM-style silence pattern briefly at the start of Native DSD playback–in that case, the reason for artifacts was that kernel bug. That bug has since been fixed, but if you are specifically having a problem only when beginning Native DSD playback, and not other other circumstances, it might be worth investigating an upgrade/kernel patch to address it.