Hello Mark,
You are right about the scenarios.
Just, BOE (or BO), you have to be aware that some functionatilies will not work as BI Java.
Example. ODOC, Bookmarks, BEx Broadcaster.
I don't remember, by heart, anyother example.
I don't know any documentation guide, since this is more installation. I work with issues own BW and BI Java side, so everything I know I learn during these years on this area.
Maybe there is something on PAM (http://service.sap.com/pam) and on the installation guides (which I don't know the direct link).
Best regards,
Edward John