Why said they need to make the spread of the bullets even matter? Just make it so the bullets hit AROUND the point of attack. Bamn, done... fixed. None of this Super Soaker Machine Gun buisness.
Actually it is a problem with a lot of it in general and suggests a lot of cut corners due to a deadline. Why do they have weapons that shoot multiple visable shots if they arn't going to handle those individual bullets well?
Which is my vote: Originally they were going to handle each projectile individually but they ran out of time.
Post script,: adding this in since you edited your post at about the same time I finished mine, so missed this.
Given that they have had 4 years, I very much doubt they needed to cut corners with making it work as a stream versus making it work as multiple projectiles though. It means new art assets have to be made for their shots, which isn't going to save you time, compared to just using the same bullet asset that would have been available for each weapon. From an artistic standpoint, it makes every weapon very distinctive, useful to know if you're being attacked from beyond line of sight.
And given how the system works, with cover effectively being an evasion bonus, then working that in there is a needless complicated headache. I'm going to stand by my point that it doesn't play well with other mechanics such as cover and lightning reflexes. If we're dealing with realistic amounts here, a machine gun (Specifically M60, going by the in game model) should fire 30 bullets in a 5 second burst. With a little deviation, that's a cone of death, alien menace over.
Simply put, it's very hard to make something like this work with the hitpoint system, the cover system, the overwatch system, the perk system, and the damage system without it snapping the game in half.