In an effort to sound dumb, I have to ask what should be an obvious question.
On page 10 of the AT45DB081B datasheet table 1 list 10 different opcodes for various read commands. If we just take one as an example:
"Buffer 1 Read" has two possible Opcodes 0x54 and 0xD4
0x54 is for "Inactive Clock Polarity Low or High"
0xD4 is for "SPI Mode 0 or 3"
From the Atmega128 datasheet page 169 it would appear that "Inactive Clock Polarity Low" is in fact SPI Mode 0!!!
Similarly "Inactive Clock Polarity High" is in fact SPI Mode 3!!!
So what am I missing? Please be gentle. I know it's something obvious.