1st: The instruction states the player receives extra oil plumes and these are placed in his storage tanks. Does this mean the player just gets to put the plumes in any of the three company? There's no need to do the "Extract & Transport Oil" step? If that's the case, that seems very powerful - getting free oil and not worrying about the location of your train or having to pay anyone to transport it.
You've read it correctly. It may seem powerful, but it's only 1 or 2 extra oil plumes (not a sustainable source of plumes). Also, the cards that this special action occur on are not particularly high in either movement points or license cards. So, you're getting a quick splash of oil at the cost of better setting up your long term oil-production infrastructure. Also, unless you've already stocked up on license cards in a previous turn, good luck trying to sell them!
2nd: The instruction also states that placing this oil in the storage tanks MUST be done before the END of the Prospect and Drill for Oil step. What exactly does that mean since (in the Prospect and Drill for Oil step description) it states Special Action always is performed last anyway. I'm not understanding this since isn't that already a given?
Yeah, that's not strictly necessary. Perhaps it's there just to remove all doubt of when the plumes must be placed. Just to ensure that the player can't hold them in reserve until they win an auction, or in case a player further down the line has a "price fluctution" special action that they might vindictively play on the oil company that you place the extra oil plumes on...