The only time it would matter, as i see it, is if a coin is mined just a few minutes, so that a small miner does not even get one share submitted. But then again, it would not be a big deal, statistics dictate that what you lose in one period is made up for in another. So all you loose is the difference between profitability between the two coins mined.
For faster coins, if you cannot submit 1 (high difficulty = 512) share, you get paid nothing. So if we mine those coins for 1 hour, the slow miner will earn nothing during that period.
Is that share mined by a single GPU or is it distributed by all GPUs in one rig?