Turning every core traitline thats equipped on the third traitline to get a boost in power
Like Engineer Alchemy Traitline on the third traitline would get a + (Alchemy+) Transforming some traits or empowering traits
To empower the core traitlines
This isn't a great idea simply because this would prevent the developers buffing individual lines in the future.
However your idea that the game recognizes if you have an elite spec equipped, similar to the buff core rev recently got, certainly has potential. The most straightforward way would be to give each line a corresponding stat bonus of say 240 (weapon traits with that weapon equipped) or a simple +180 every stat. It's not much, but it would allow core builds to specialize into specific stats and therefore fill niche roles better.