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I have just successfully installed EM12c with the exact issue/question. Please did you get any answers or can someone help?
The gcstartup script creates entries at run level - 2,3,5 and reason is that we are not sure machine will come up on which run level so we place it in 3 levels making sure EM will come each time server is rebooted. This behavior is same since 10g EM. If you are confided that your machine will always come up on run level X then you can change it else i will suggest leave it there.
Any particular reason or concerns with having entries in 2,3,5 run level ? Or this is just a curiosity question ?