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Alex,
I am creating a seperate thread for your query as you had posted on a query that was closed so it is harder to track.
Your understanding regarding the use of serial flash utility is accurate as far as it usage on the TI supported EVMS and LCDK is concerned. These utilities were sample utilities created to support flashing on TI EVMs and LCDK boards. If you are trying to use this on a custom hardware, you would need to modify the SFH utility so that you ensure that the configuration matches your own hardware. Here are the list of recommended modifications we recommend on custom hardware: Specifically for SPI flash, you need to verify that you are using the correct clocking, SDRAM and SPI flash command and size settings.
Hope this helps.