Honestly, I don't even know how it works. Could you elaborate a bit, please?
As Riddler said, spread is completely independent of how long the bullet takes to get to the target. Leading shots is good, random spread is bad, and there's no reason they have to be paired. For an analysis of how Halo 3's random spread can influence the outcomes of even gunfights with perfect aim, read this post.
Bungie's explanation for random spread:
In Halo 3, each bullet from the Battle Rifle’s three-round burst is networked individually under the cases outlined above. Additionally, each bullet has a different margin of error, with the first round from the Battle Rifle being the most accurate of the three bullets. The first bullet can have an error between 0 and .15 degrees off of the true aiming vector. The third bullet is between 0 and 0.38 degrees, the second bullet falls somewhere between the first and third. It is a mistake to look at where the third bullet lands and assume all three bullets are that inaccurate. The outliers (0.15 on bullet 1 and 0.38 on bullet 3) are the absolute worst-case scenarios. In that context those numbers don’t mean a whole lot – but in the grand scheme thing of how the Battle Rifle operates, they are pretty meaningful.
The Battle Rifle works this way because after Halo 2 it was retuned to be a reliable headshot and anti-sniper weapon (in terms of pinging Snipers at distance from their scoped-in state). The first bullet in the burst fills this role – it is quite accurate (identical to the Halo 2 BR, but with a travel time), and will kill an unshielded unit with a headshot or ping a sniper.
Another design goal with the Battle Rifle in Halo 3 was to bring the kill-range closer. One way this was achieved was by giving bullets 2 and 3 from the BR a wider error, which makes them less likely to land outside of the BR’s intended effective range. Summarily, this reduces the BR’s effectiveness AND damage output at those ranges, without compromising its ability to finish a target at the same range.
This change allows the Battle Rifle to be competitive in terms of damage output at closer-than-Halo 2-levels, without being so effective at longer range, that players caught in the open are gunned down too quickly (that task in Halo 3’s sandbox belongs to the Sniper Rifle. If you need to control a space 30wu [world units] away, use it instead).
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Much of the fervent debate comes from players who simply want the weapon to perform differently than it was designed to perform. The bullet variation in the Battle Rifle’s three-round bursts is a design choice that further defines the weapon's role in the Halo 3 sandbox.