The theory behind a score based system assumes that you're continuously mining, and continuously submitting shares at roughly the same average speed (give or take some variance) in order for it to be fair, after an extended period of time... and it is. I'm not questioning that.
Just to clarify,
It has nothing to do with continuously working. The difference in variance tightly converges with the number of shares submitted throughout the entire lifetime of the Miner, completely regardless of how often those shares are submitted. You could have it running only a few hours a day, and the variance difference will still converge at the same rate per share.