Sorry for the delay on this.
1 & 3) I believe they all use the ViewportAPI.schedule_capture API under the hood. You can see it used directly in omni.kit.viewport.utility.capture_viewport_to_file(). I would take a look at the MovieCapture implementation though to understand the timing for making sure the stage is loaded and sampling is finished.
2) Can you share an example of the output? Are you using instanceable=true for your assets that are being instanced?
3) When you’re make a lot of updates programmatically, the USD update events can become a bottleneck. We’re developing usdrt to give you a faster runtime experience. The API is similar to working with USD, but it updates the Fabric runtime data instead: USD, Fabric, and USDRT — usdrt 7.1.0 documentation