I'm not sure if the numbers work out the same (a quick check indicates an average roll would have the same margin of success/failure, but I'm not sure if it applies at all points, especially when it comes to things like Natural Aptitude), but there's a much simpler answer.
And that's because ATOW works on a fixed TN system. Its core mechanic is that you don't change the target number. The TN is always fixed, and its always the roll itself that is modified, whether you're making a Skill Roll or an Attribute check.
So to keep the core mechanic, rather than changing it up for certain situations, when it comes to TW modifiers, you subtract them from the roll, to keep the same mechanic across the RPG.
There is an instance when the Target Number itself is modified, and that's the phenotype bonus for Clan characters, but even that's just changing the base TN forever, rather than modifying it each roll (a matter of semantics I know, but there you have it, and it keeps the core of "fixed TN")