Well, it's not the alternator because the Prius has no alternator. It doesn't have a starter motor either.
Eco mode just changes how the gas pedal travel works. That is in both eco and non-eco modes zero is zero and floored is floored, but in eco mode half pedal is like quarter pedal in non-eco mode. It won't make any difference in noise level.
My guess (and long distance diagnosis for vehicle noises is only guessing) is that the tires are unevenly worn and causing the noise. There isn't anything else in the back to cause an "engine like" noise. The two motors and the engine is in the front. The battery is behind the rear seat but the only noise maker is a cooling fan that only runs part time when the battery compartment is hot. I've never been able to hear it on my Prius, but I suppose a fan that has a bearing going out will make a noise, though I wouldn't think it would sound anything like an engine.
My second guess is that there is a hole in the exhaust. Rental cars usually aren't driven with care.
Typically the main noise that you can hear in the Prius is the tires/road noise. It's never been a problem in the 120,000+ miles I've driven mine.
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