I realize there are special deferral rules for performance based compensation under 409A. Would these also apply to the short-term deferral exception?
For example, assume a bonus is based on an "employment year" not the calendar year or the employer's fiscal year. Can the bonus be paid out a short time after the end of the employment year (assume, for example it runs April 1 to March 31) and still be considered a short term deferral?.

I don't think you have to go to the performance-based-compensation rules. If the bonus has standard features such as must be employed on the last day of the employment year, then the right to payment is subject to a substantial risk of forfeiture until that date (i.e., March 31). If the payment is made before March 15 of the following year (possibly later, depending on the employer's taxable year), the payment will satisfy the short term deferral rule. See 1.409A-1(b)(4)(iii) ex. 4.

If the bonus is not subject to a substantial risk of forfeiture (for example, if the bonus is X% of widgets sold during the month) then the short-term deferral rule won't apply (unless the employer has a fiscal taxable year that approximates the employment year) -- because the payment that vests during April-December of the employment year will not be paid within 2-1/2 months after the employee's taxable year.