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The current approach for the ILM Assistant does require a copy on every instance. We're aware of the need and desire to manage multiple instances from a single node, and we've placed this requirement high on our wishlist.
As for APEX requiring the database instance to shut down .... hmmm ... I don't recall having to do this after an APEX install. I suggest visiting the Application Express forum and posting the question there.
All you need to run the ILM Assistant is APEX, formerly known as HTML Db and a web server which is required by APEX. Although with 11g you can use the PL/SQL Gateway instead of the web server.
I am not aware that you have to shutdown the instances as they need to be up to install APEX into the database.
No it does not modify the Oracle binaries.
Also just to clarify, you don't have to shut the database down to install APEX (it's really just a precaution incase someone is connected and doing something that could interfere with the APEX installation).
I have performed lots of APEX installs/upgrades without shutting the DB down first (and then bringing it back up of course).
Hope this helps.