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The "FF" are an erased, erase block that has never been written to.
(Flash erases to "FF" not to "00").
The iROM code (used to initally load or re-load an external flash device) only works in 512 byte increments so those "00" may be 512 byte block padding.
Check the boundaries of 512 byte increments for differences, including differences in padding.
Ah, yes, the first blocks of the flash are "in use", they are "in use" by the SoC on-chip firmware. The SoC reference manual includes the "memory map" of what is what there.
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