If its EET compatible you can install it manually after. Just keep in mind that mods that need to reference .DLG files might fail to install due to the .DLGs being altered when EET_end runs.
You shouldn't have any problems installing Pai'Na though.
If you install NPC mods after EET_end you may get errors or in-game oddities if those mods either have interjects with other NPCs or ToB or BG1/SoD content. In such cases you would need to uninstall EET_end, install the mod and run EET_end again. Normally that is not a problem unless the mod you add has some other dependencies.
PS - mods not appearing in BWS may be due to the fact that the author decided not to commit them to BWS.
I went through the entire K4thos' list and BWS list and found that some mods in the former (Tome and Blood, Palemaster) are referenced inside BWS as deprecated in favor of EET. I'm assuming then they should be removed from K4thos' list. On the other hand several mods are not present in BWS: Ajoc's minimod, Bardic Wonders, The spellsword, Mystic Fire Paladin Kit, Pai'Na, Sheena, Southern Edge, Evil Kits and Solaufein's Rescue. So my question remains: is there a way to "inject" mods in a BWS install? Because installing them after it would just miss all the streamlining offered by IR, SR, SCS, SoB and all the mods intended to balance the game.