The difference is mainly shift tables and line pressures. With a proper tune, the non-perf shift tables can be tuned for MPG and the perf shift tables for performance. That way you get even better dual use from your vehicle.
Perf shift is a 'shift on the fly' thing.
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'13 Mustang 3.7V6 - MT82
'00 GP SE (L67 Swap, XP, Headers, 3.25")
'98 GTP, '01 Bonne