new-entity uses the file you already found.
generate-entities uses the templates in hibernate-tools so if you know how to use hibernate tools you can customize that ;)
p.s. i hope we can add reveng.xml support (or something similar) to seam gen so we can give you the full control over what is reverse engineered (in this case the wanted id generator)
Reverse engineering uses freemarker templates. The ones for reverse engineering entities are packaged with Hibernate Tools. You can customize them. Check the Hibernate Tools docs.
Ah, makes perfect sense, now that you point it out. My mind was being to narrow, thinking that the scope was entirely within the Seam source. Thanks for the quick response.
To avoid having to answer this question time and again, you might just want to add that hint to the usage statement in Seam.