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When does the ISR mapped to SPI_STC_vect (SPI transmission complete) get fired? Does it fire after a byte has been received (eight clock cycles) of when the slave select changes back to high to deselect the slave? Or: does "transmission" mean the transmission of a byte or the whole bunch of bytes that belong to the command sequence?

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It fires after a single byte has been sent or received (the two are one and the same). This is because there is only room for one byte in the buffer, so you need to get it out of that buffer (or put a new one in) after each 8-bit transfer.

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