Question: Is it possible to transfer data IN/OUT over multiple endpoints in FX3™ simultaneously?
No, this is not possible on any USB device, including FX3. The USB 3.0 protocol is full duplex with a 5-Gbps signaling rate on each TX and RX data line, but when one of these lines is transferring data, the other line is only transferring handshaking or link-related packets. Both of these lines do not transfer data at the same time.
The host application that handles data transfer can have two or more threads that seem to do simultaneous data transfers over multiple IN/OUT endpoints, but the transfers actually happen in a time-multiplexed fashion. This approach that uses multiple threads in the host application permits bi-directional data transfer, if it is required.