В даташите есть комментарий к таблице Supply Voltage Thresholds for Power-On Reset .
VCCINT, VCCAUX, and VCCO supplies may be applied in any order. When applying VCCINT power before VCCAUX power, the FPGA may draw a surplus current in addition to the quiescent current levels specified in Table33. Applying VCCAUX eliminates the surplus current. The FPGA does not use any of the surplus current for the power-on process. For this power sequence, make sure that regulators with foldback features will not shut down inadvertently.
Понимаю так, что мелкосхему не убьёть, а ейное питание как получится.