Dynamic counter values for PLL

I believe you need Quartus to make the configurations, but you can store them in your design and have your design load/reconfigure on the fly without Quartus. As I said, there's a big difference between M, N, etc. and configuration bits, and Quartus does that whole conversion(as well as Design Rule Checks) for you. It makes the .mif files, which you then use to program it. So if you wanted a "limitless" number of configurations, you will probably have trouble, but a known, bounded number of configurations is doable.