The "S" engine has the turbo (nearly as hot as the actual exhaust manifold itself) right on top in the front of the engine compartment, so when you open the hood, it's the nearest item to you. So yes, you WILL feel heat, and that is not necessarily an indicator of a problem, but let the dealer reassure you on that point.
As to the battery issue, some questions here:
Are you powering your iPod from the car? If so, is the outlet you are connected to live when the key is turned off? If not, you may be surprised at the number of OTHER systems in the vehicle which are also powered up with the key on, which are more likely to be a source of significant current drain than the iPod.
Assuming you are not listening to the music on ear buds, you must also have the car stereo system powered up plus whatever else comes on at that condition.
Given the vintage of the vehicle, I'd certainly be inclined to letting the dealer have a go at setting things right. That's why the pay them the big bucks, you know!

Bob