About VCCIO, VCCPGM, VCCPD for Configuration , genernal I/O pins at same bank

That sounds exactly right to me. If you're trying to 'Force VCCIO to be compatible with configuration I/O voltage' then yes, the voltage on VCCIO will need to match that of VCCPGM. However, without that requirement, it won't.

Refer to page 18 of the cyclone® v device family pin connection guidelines (https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/dp/cyclone-v/pcg-01014.pdf). This specifies the requirements for VCCPGM & VCCPD pretty clearly. In respect of the VCCPGM pins it states:

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When these pins have the same voltage requirements as VCCIO and VCCPD, they may be tied to the same regulator.

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However, if they have different requirements, they need not.

So, yes. You should be able to power bank 3A from 1.8V.

Cheers,

Alex

PS. Just to add - and confirm - I can put a project together with VCCPGM @ 3.3V & VCCIO 1.8V. VCCPD3A must be 2.5V. It's perfectly valid.