I've finished the BG1 portion of a heavily modded EET run, and frankly it was an unbalanced mess (and I found out that EE Setup was... not well regarded), so I want to start SoA over with a fresh installation and better curated mod selection.

Given all that, do mods that say they're for EET typically require EET even if they only add SoA/ToB content, or should I be okay just reinstalling BG2EE and modding that?

each mod is different but in general mods witch require EET should clearly state that up front... there is a list

https://k4thos.github.io/EET-Compatibility-List/EET-Compatibility-List.html