Data packet format when USB initialized as COM port
The COM port is either a USB CDC device, implements a vendor specific protocol, or both.

These are high-level protocols on top of USB endpoints, so the wire protocol for the actual data transfers are most likely to be BULK OUT and BULK IN packets, with a few CONTROL transfers interspersed (so USB packets do not correspond 1:1 to data transfers over the virtual serial port).

The USB wire protocol is fixed, because the exchange of data and acknowledgements must happen in a short timeframe, and will follow the same pattern regardless of what device classes and interfaces the USB device implements.

To address your use case: it is unlikely that the USB will be the bottleneck.