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Strange, is this for the initial prototypes only? If it is for production, then it is not advisable to deliver boards which does not work.
If you claim that it is easier to produce a board without any external bus than a board with an external bus it makes sense.
If you want to have increased possibility to test a board with internal flash and external bus, which proves faulty, then JTAG works. If the clock is working, you can download to SRAM and do tests there.