The game has a few .2da files(savecndh.2da for halflings, savecndg.2da gnomes) that the game uses to add all the special save throw. When you install the component, the mod just copies over the files with it's own. The Atweaks has it's own files. Now, they could all be same and you wouldn't even notice... or the difference is 1 or 2 at most so... that's out of 20 dye, so you won't mostly even feel it, ever.
In case of gnome 2 are substracted from Wand and Spell saving throws. With Spell Revisions installed I have found no way to make the constitution bonus count. Which at con 18 equals a saving throw bonus of 5. So quite the difference. Especially for BG1.