I did not think that was the case. Again, the hard IP is the same. I opened both versions, launched altlvds_rx megawizard/qsys for Cyclone V, made the deser /8, clicked on external PLL and they both say the same thing. Can you copy the two messages your looking at here and also put where they're coming from?
I think there are multiple ways to do it as long as the relationship stays the same. I'm almost postiive the frequencies must be the same between versions(one fast, one parallel, and one parallel with small duty cycle for enable)