First off to House Repair Talk!
Now, about your roof, E.P.D.M. is a commercial material and is NOT warrantied on ANY residential application. If the roofer you are talking to wants to install a non-warrantied material, doesn't know how to flash a pitch pocket around a post, you need to find someone who understands what this is and can do it. If you bolt a 4x4 to the ceiling joists, repair the decking, you can fabricate a pitch pocket thats filled with a pour-able sealer. Then have a carpenter trim out the column with dimensional lumber to cover up the column and pitch pocket.