1) The Napoleonic battlefield was full of drifting smoke, therefore, did your Officers spot, and identify, that cavalry unit,
This could apply to any and all situations and there are plenty of examples that it did. So by that argument we shouldn't be able to fire at anything.
2) Your troops were taught to obey orders, with not much initiative allowed to them (except in Hand-to-Hand fighting),
First hand accounts show that infantry tended to start shooting against orders. This was particulary the case when advancing and the orders were to charge. Very often the advance would falter and firing would start. Once firing began officers often had a difficult task stopping it.
3) Your troops were taught to shoot to their front, and not to take aim,
Very true.
4) The ground is not flat, but undulating,
And this applies in all situations and so would mean a lot of 'targets' could not be seen, not just cavalry riding across your front. It also means that units could get very close to you without being seen viz von Bredow at Mars la Tour. All war-games tables are too flat. Something to with figure scale not matching ground scale. A 1mm dip in your table would be enough to hide an infantry battalion from sight.
5) With enemy Cavalry that close, you would more than likely be in Square (600 men divided by 4 [sides] divided by 3 [ranks] times 2 [front and middle ranks shooting] equals 100 men shooting across a frontage of 33 yards 1 foot [30 metres] frontage). The cavalry unit, at 20mph [30kph], would cross your frontage in approx 20 seconds (2 ranks of cavalry). Therefore, 100 musket balls in the general direction of the passing cavalry unit. You may hit 1 or 2 troopers, and/or their horses.
(NB. 6oo men per Battalion, with 2 foot [60cm] frontage per man).
But the point of the question was that the infantry unit is not in square but in say column or line.
It is possible to rationalise away any anomaly by postulating a set of circumstances that would explain it. But here we are examining a possible set of circumstances where a line or column of infantry has cavalry in abreast or waves ride across it in clear view. If waves then the flank would present considerably more than two horses depth, and if moving at a normal pace would be in view for some time.
Ultimately I don't think it is that important as it will come up very rarely. The rules are an abstraction at a level where these issues are not a material factor. Personally if I was worried about the level of abstraction I would use a different rule set. However, I like these rules because they are at the simpler end of the spectrum yet still give a very good overall feel.