If the first rank men were standing, and the soldiers had their backpacks on their backs, the third rank men could not fire effectively, while the muskets of one rank were usually kept loaded to the most critical situation.

What is effective fire against cavalry, fire at close range and to have a fire reserve - so the horseman knew - the closer he comes the more dangerous it gets, because there were always some soldiers with muskets at the ready. It wouldn't matter it the fire of the third rank is that super effective - as long at it it potentially there - it will be such a great physical thread - and an even much more psychological thread, that the trooper won't be willing to charge home.

what has he to fear from a kneeling row of infantryman who cannot shot back? Or behind them - unloaded infantry?

Also in case against cavalry, you were shooting at a higher target and 3rd rank, in my view - could bear the muskets well enough, at least so well that cavalry wouldn't dare to charge home, as long as their muskets were loaded.

A first rank standing - with leveled bayonets - at least seems to be at least a more threatening obstacle than a kneeling one.

So it was one of the reasons to attack a corner of a square - because only a limited amount of muskets to bear, or to find ways to induce the defending infantry to fire all together prematurely (Prussian cavalry tactics of 1806, which failed miserably)