Sure, F&F has some generalizations. When I first tested these rules out the two points below drove me crazy, too. But consider:

Richard Hasenauer wanted to depict the fluid portion of the ACW. The original book was entirely about Gettysburg. If the rule isn't there, outnumbered Confederates will choose the best defensive terrain, and hunker down. And that isn't realistic. The fact is, they behaved as though they thought they got a +1 for charging.

Fire & Fury uses a system where charge combat is difficult in any case, and normally provides minimum, though bloody, results for the winner, but is highly unpredictable in its marginal results. Then it gives the Confederates a +1 to encourage them to be aggressive. The Union doesn't need the +1 because its numbers and firepower can create excellent opportunities all by themselves.

The impact on the game is that both sides maneuver and charge aggressively, which was the hallmark of the early Civil War. The realism created here is in the minds of the commanders.

As for the Artillery, Federal guns could be counted on to have full ammo chests, and to contain larger proportions of heavy calibre and rifled weapons. The +1, at range, in the context of a not-very-bloody long range fire system, is quite realistic. At short range, as when cannon are used defensively, the advantage disappears. If the Scenario designer is careful about historical placement of woods and hills, there is no problem. It is only when wide horizons of fire can be dominated by whole gun lines of 3+ batteries that the Federal advantage becomes extreme. And that is in the whole control of the designer.

Command & Control simulation, which you don't mention here, is more problematic. The game creates the feel that those units will do what you want them to. But delays for unpredictable reasons are built into the maneuver table, which means that units will tend to follow the plan until contact is made, then behave highly unpredictably from then on. Still, while they may fail to act, or act slowly, they never do something you actually don't want them to do. Building a believable AI into one's command rules is extremely difficult, and while Richard Hasenauer is very talented. He's not a rules demigod.

It is hard to do justice to F&F, because the interplay of its parts is so intricate. But the result is a solid, smooth, fast play simulation disguised as a game. Over the years, even while working on a set of my own rules, I have enjoyed, and learned from, F&F. I really recommend it, flaws and all.