The supported modes of the PN532 chip on the NFC Shield do not depend on the interface used for communication (at least when it comes to NFC operating modes). So you should be able to send whatever commands you want over the SPI interface just as you would with the I2C interface.
With regard to the inDataExchange
command, this command seems to be implemented in the current version of the library (see the github repo).
And no, besides wiring the interface selection pins to a different value, there is no other way to change the interface mode at runtime.