It depends on the situation. I remember an issue with a certain line of 5850's were flashing the BIOS to a different brand name fixed some flickering issues. Also people do it to permanently OC a card. Since the factory using does a lot of testing and setup new rules for the fan speeds for their OC'ed cards, it is a safer bet than manually doing it.
BIOS flashes also helped with heat issues for the 4000 series by just setting the fan's normal operating range to a higher level since they were programmed not to go over 40% speed by default.
I have not heard of any one flashing the bios to improve OC results other than the fan tweaking which is BIOS editing, not flashing. For that card, I doubt it would change the OC results since it will still be the same hardware, same fan settings, and same default clock speeds (as I don't recall any pre-factor OCed 4870 X2).
I would suggest using a BIOS editor and changing the Idle, In Use, and maximum fan speeds. Then just OC it the same way you have before. With the improved cooling you should be able to go a little further.