It actually passes very close to Amaravati!! Amaravati is a famous Buddhist and Hindu pilgrimage town around 30km from Guntur in Andhra Pradesh.
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The 'far far away' place in Maharashtra is Amravati ( Easy to miss the difference between AMAR and AMRA if we don't look closely :P ). The wiki page below also mentions both the places in the disambiguation at the top.
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This train was originally between Hubli-Guntur and hence the name Amaravati express. Over time it was extended on both sides to HWH and VSG. So, no problem in calling it as Amaravati express. Most people in AP don't even know that there is another place with a similar name in Maharashtra, so no problems with confusion at least for AP people. In fact when TPTY-Amravati was introduced me and my friends were puzzled because we knew that Amaravati ( in AP ) did not have a railway station and wondered why the train wasn't to Guntur or BZA until we noticed the different name and realized that it was a different place. :) :)