You can convert a wav to nes only via $4011, not via $4010/12/13 to have a good sample frequencey (otherwise all treble sounds will be cutted).
All theese games (exept FF3j) uses only $4010/12/13, not $4011, so I can't see why just some write to theese registers can break an IRQ.
And FF3j uses this only in battles, and IRQ triggering is also used only in battle ($4011 is set only in the NMI code, I think).

Bregalad, Ent from the woods of Fangorn