>> When I do this and probe the sensor's MIPI stream I confirm its output frame rate has indeed dropped to 25.2 fps as expected. Using the CX3 configuration tool to generate new settings for the reduced frame rate doesn't change any of the settings that I was using at 48.4 fps
Since you reduced the fps, there may not any changes needed in MIPI receiver configuration. This is fine.
Please do the following and confirm
1. Probe the VSYNC test line and check whether it is as per 25.2 fps
2. Confirm whether there is data flow between GPIF II producer and USB Bulk IN Endpoint
3. Capture the USB Trace with Wireshark and check whether there is any data flow between Cx3 and host