[ModelSim] How to set design files to be recognized as SystemVerilog also in Modelsi?

Yes. Refer to my last post in this thread (http://www.alteraforum.com/forum/showthread.php?t=54455). This shows you how to add Altera libraries to your ModelSim simulation. Quartus does 'hold your hand' a little in this respect when you run your simulations through it.

I'm afraid I've no experience to offer with regards to NativeLink. However, I'm pretty sure it will rely on you constructing your project in a 'standard' manner, with files with the 'correct' suffix. Having a quick look here (https://www.altera.com/support/support-resources/design-examples/design-software/simulation/modelsim/exm-ncsim-native-link.html) it doesn't look like it gives you anything over and above the standard Quartus install. Maybe I'm missing something...

Cheers,

Alex