Hello,
using 2.5V for JTAG interface is an Altera suggestion from Cyclone III manual respectively AN466
cyclone iii design guidelines. It hasn't been invented in this thread. There are understandable reasons for this suggestion, but is also obvious that it doesn't fit all applications. Basically, configuration interface (including JTAG) can use VCCIO up to 3.3V as with previous devices if some precautions are observed.
With AS configuration, 3.3V VCCIO in the respective bank should be used, cause EPCS devices use 3.3V supply, the same with 3.3V standard flash in AP Mode. That's what the quoted knowledge base entry says.
With AS and CIII, you have two options: The traditional combined circuit, requiring separate configuration connectors for AS and JTAG, the AS part as shown in figure 10-28 or the new "smart" CIII variant, programming AS device through a SFL JTAG instance, as in figure 10-29. (I assume, that JTAG interface should be always present for development and test support) You may ask, why the two figures don't clearly set AS VCCIO to 3.3V as requested by the knowledge base? I don't know.
Regards,
Frank