According to the design notes for the Spartan6, the power rails can be brought-up in any order. However, I believe it's still a good idea to sequence properly.
Now, the question is what should happen when you have multiple VCCO sources? Can the output voltage regulators be brought up at once? I believe this is the case.
I'm using a TI LM3880 for power sequencing. I would assume that there wouldn't be an issue connecting FLAG3 to the ENABLE pin of four regulators since the signal isn't driving anything. Is this the case? I'm not seeing anything in regards to output current for the FLAG signals in the datasheet.
For this design I have three different voltage levels for the FPGA and since it's a development board design, I'm powering the microcontroller with a separate power supply so that I can pull-off some shorting resistors and get an accurate idea of how much current everything is pulling.
In the end this will be a battery powered application.
LM3880 Datasheet
http://www.ti.com/lit/ds/symlink/lm3880.pdf