ATX supplies provide a PWR_OK signal that indicates when system power supplies are stable. This signal is asserted at least 100 ms after actual supplies are stable. Thus, this extra 100 ms can be added to the timing margin.
50 ms (T POR ) + 33.2 ms (bitstream time) + 2 ms (ramp time) - 100 ms = -14.8 ms
-14.8 ms < 100 ms PCIe standard (okay)
In this case, the margin is 114.8 ms.