An isolation test is performed on an interface connector to verify that all unrelated signal pins are not shorted to one another. For example, between signal x and signal y or VCC and ground.
Looking for guidance on what resistance to expect when measuring between VCC and ground of an unpowered complex circuit with several ICs including a large FPGA. Should I expect to see a resistance as low as 30 ohms?

 

If you are just checking there are no shorts between the lines then you might measure with a very low voltage, like 0.1V, so semiconductor junctions are not turned on.

 

Are you testing the board or the FPGA?
You might want to read "JTAG test". You can use the FPGA to test every pin on the FPGA and what the FPGA is connected to.
Us the JTAG port to program the FPGA or to run tests.
The test is simple. The port has Data_in, Data_out, Clock, load....
Set all pins low, read all the data back. Then you do a waking bit test. "0000010" Where all bits are low and one bit is high and walk that bit through all pins. The a waking bit "1110111" where all are high and one is low.
The PC looks at the data coming back and can tell if two pins are shorted or if a pin is stuck high or low.