Like I said, Altera/Intel doesn't really specify a powerup order for the Cyclone series.
However, if I was designing with a 500$+ Stratix FPGA, you better believe I would scrutiny every ounce of the data handbooks.
If there was a problem, like with one of my Analog devices HDMI RXD / sampling processors, the chip gets hot and a regulator may burn up as the IC draws too much current on a supply rail and fails to function, or it just doesn't do anything at all. I bet if my regulator was strong enough in this situation, the IC may have been blown.
It does specify for Cyclone V:
Power-Up Sequence Recommendation for Cyclone V Devices
Figure 10-3: Power-Up Sequence Recommendation for Cyclone V Devices
To ensure the minimum current draw during device power up for Cyclone V devices, follow the power-up
sequence recommendations as shown in the following figure.
Power up VCCBAT at any time. Ramp up the power rails in Group 1 to a minimum of 80% of their full rail
before Group 2 starts. Power up VCCE_GXB and VCCL_GXB together with VCC
Power Up
Power up all the power supplies that are monitored by the POR circuitry. All power supplies, including
VCCPGM and VCCPD, must ramp up from 0 V to the recommended operating voltage level within the
ramp-up time specification. Otherwise, hold the nCONFIG pin low until all the power supplies reach the
recommended voltage level.
For Cyclone IV:
Power Up
If the device is powered up from the power-down state, VCCINT, VCCA, and VCCIO (for
the I/O banks in which the configuration and JTAG pins reside) must be powered up
to the appropriate level for the device to exit from POR.
Power-On Reset (POR) Circuit
The POR circuit keeps the device in reset state until the power supply voltage levels
have stabilized during device power up. After device power up, the device does not
release nSTATUS until VCCINT, VCCA, and VCCIO (for I/O banks in which the
configuration and JTAG pins reside) are above the POR trip point of the device.
VCCINT and VCCA are monitored for brown-out conditions after device power up
Devices Driven Before Power-Up
You can drive signals into regular Cyclone IV E I/O pins and transceiver
Cyclone IV GX I/O pins before or during power up or power down without
damaging the device. Cyclone IV devices support any power-up or power-down
sequence to simplify system-level designs.