Can the USB Controller on the FT90x Host other FTDI devices like FT-X and FT Series?

Yes, Bridgetek have produced an example FT90x UART to FTDI’s FT232 Host Bridge application.

This example demonstrates bridging an FTxxx class device (e.g. FT232R, FT-X Series) present on the FT90x USB host port to a UART interface, with data transferrable in both directions.

Note: since the USB commands that are used in order to control FTxxxx devices would be exposed, the library is provided as precompiled.