The speaker depicts the train on a scale larger and more powerful than a mountain range – pretty heavy duty. It's described as "prodigious," and it is clearly something of a prodigy, as it's able to lightly "step" around a "pile" of mountains like a child stepping carelessly around a pile of toys.
And supercilious peer In Shanties — by the sides of Roads — (6-7)
If you had any doubts about the train's strength relative to our own, let them be erased here. The train clearly views itself as superior as it passes by human habitations, a sentiment betrayed by the adjective "supercilious."
And then a Quarry pare (8)
As if the train didn't seem powerful enough already, the speaker demonstrates her awe of its physical strength here – it easily "pares," or slices, through rock as it passes through a tunnel.
And neigh like Boanerges — (14)
Boanerges is a kind of nickname Jesus gave to two of his disciples for being super-fiery and bombastic preachers. It means "son of thunder." To say that the train's "neigh" is like Boanerges depicts it in pretty mighty terms.
[…] punctual as a Star (15)
The movement of the stars in the sky has long been seen as one of the constants of the known universe. This comparison to the stars implies that the railroad has now become as powerful and trustworthy (and out of human control?) as the heavens.
[…] docile and omnipotent (16)
Hmm, need we really say more about this? The word "omnipotent" kind of says it all. This train is the most powerful thing out there.