Use the TrueLVDS if you are getting close to the bandwidth limits of pairs.
The emulated LVDS IOs still work fine at lower frequencies (available on all banks). Its less about the voltage ranges and more about the bandwidth and tightness and jitter. If you want the >500mbps, you should probably stick with the TrueLVDS, though, I have overclocked the Cyclone series emulated LVDS to 1gbps, bidirectional error free.
Also, if the FPGA is the master clock generator and output driver, you can easily get away with maxing out the specs. If the FPGA is the clock generator and you are receiving LVDS, timing constraints become crucial.
You can still run the emulated LVDS at 3.3v IO levels, but again, this is not officially supported at 640msps.