Ok I updated to 1.3 (only BGEE not BG2) and manual launched EET is now running.
I will just quote the readme:
Required:
The BG2:EE installation (patch v1.3 is required) should be a "clean" installation. Translations and voice-overs are of course allowed but installing other (especially larger) mods that changes DLG and BCS files, before EET, may cause problems with later patching, so it's better to keep the installation as clean as possible.
The BG:EE installation (patch v1.3.2053 is required) should be either "clean" installation or with any combination of mods listed in the F.A.Q section.
It's very possible that you will encounter error during installation as you REALLY need latest versions of both games. Either way BG2:EE previous to patch 1.3 was literally unplayable (game braking bugs), so I would update the game even if the mod will be able to install successfully.