I guess you're referring to serial flash programming with "second JTAG port"? It's not required, because the flash can be programmed through the FPGA by indirect JTAG programming. The respective circuit in the Cyclone III hardware manual is Figure 9-30 programming serial configuration devices in-system using the jtag interface.
Altera suggests to use the 2.5V VCCA supply instead a 3.3V VCCIO for the JTAG supply, mainly to reduce the risk of overshoots above the maximum ratings. But the JTAG interface can work with 3.3v according to the device specification. In so far, both are correct.