I read it just fine. Like I said, the DM can take care of range penalties, firing-into-melee penalties, and cover penalties. These are not things you as a player have to track yourself. All you have to know, is your attack bonus, and thats it. If you're shooting outside your weapon's range, tell the DM and let him take care of it.You clearly didn't read the example. The first step, that resulted in "a total of +9", that's the static bonus! Everything else is in flux
Range penalties, firing into melee, cover penalties, happens in almost every fight
Range penalties only occur if you have to shoot outside the range increment of your ranged weapon.
For a throwing axe this is 10ft.
For a Dart, light hammer or a spear this is 20 ft.
For a sling or hand crossbow, this is 30 ft.
For a shortbow or javelin this is 60 ft.
For a light crossbow, this is 80 ft.
For a heavy crossbow this is 120 ft.
So I think its fair to say that most ranged weapons in 3.5 are anywhere between 30 ft. and 80 ft. That is a long distance. In any given dungeon, I rarely see fights where you have to cover more than 30 ft. of range. Also, if you have to bring a ranged weapon in 3.5, you'll usually bring some kind of bow. Almost all of these have a range of over 60ft., which is more than you need for most fights in 3.5.
I'm currently running a pirate campaign that adds flintlock firearms into the mix. Most basic flintlocks in my campaign have an accurate range of about 50ft., and yet still the range increment rule barely comes up. And that is in a campaign where most opponents have firearms.