I believe you can do different VCCIO with either. The dual-supply requires two supplies to function, while the single supply lets you drive it with one, and then it internally generates the second supply. I believe this is to help with really low cost scenarios. The downside is the single-supply has much lower specs. For example, if you look at the data sheet you will see specs for both:
https://www.altera.com/en_us/pdfs/literature/hb/max-10/m10_datasheet.pdf If you look on page 29(and other places) the DSP and RAM run much slower in the single-supply device. It seems like a large trade-off, but I know one user who put the SS device in all their systems, it's doing slow speed stuff and working great.