The choke has to handle the current *and* function at the frequencies involved. So a common mode choke designed for AC powerline applications usually does not perform as well as one that doesn't have to handle the low AC frequencies plus as the high frequency switching noise. Unless there is an explicit reason not to use the app note component (won't fit, hard to get, etc.), use the app note component. You don't know if it took Wall 6 months to settle on that part as the best for the job, or it it was the first thing they tried and was good enough to stop looking further. Either way, it usually is risky to move away from manufacturer-recommended parts.
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