You can use any IO pins for any memory, however, the DQ pins have a fast latch enable, and were designed to take 2 sets of D latches at 180 degree phase, plus then 1 third set to parallel the data so the x bits IO becomes 2x bits at the half clock speed, everything time 2 for the output direction as well. The DQ pins in each bank also have a faster grouped output enable to swap IO direction as fast as possible + a dedicated high speed input Data Latch enable for recieving that extra 1/2 less clock cycle on data reads.
Once again, Quartus wont care is you use any IO, however, you get a F-Max and DDR speed penalty which is described in the IO memory interface section of each Cyclone type data sheet. I've successfully made a DDR system extra wide data system a few years ago on a EP3C55-480 pin bga, using all the IOs on the faster top and bottom banks, reserved the PLL differential outputs to clock the SODIMM modules, but had a limited 165Mhz, or, 333mhz DDR instead of the top 200/400mhz the chip was capable of. I'm sure it might have worked faster, but I would violate setup times and chance memory errors, but, I had 256 bit DDR memory instead of the maximum recommended 192 bit as per available dedicated DQ io pins. The end result was I was still getting a little better performance due to the wider 256 instead of 1 sodim which would have been a 128 bit system at 200mhz.