Applejack wouldn't carry a heavy tree too far so we can safely assume the station was in Ponyville.
Also, given the density of the train net shown throughout season two we can also safely assume it was already operational throughout the continent much earlier than season one.
Indeed, we can assume that the train in Over the Barrel was the older version of the Friendship Express which got phased out and had seen its last use on the indeed newly built Appleloose line. We can assume the line was new as the ponies had to pull the train itself, likely due to the necessary coal and water re-supply depots not having been operational yet. And of course, the town was newly built as well as hinted to in the episode - though the Friendship Express generally seems to travel to all sorts remote locations with no settlements closeby so that alone wouldn't confirm it.
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