It’s safe to say that the events of the movie reinforced, if not even created, the relations between ponies and hippogriffs. In general, as the Equestrian ponies were reaching out to more and more other species, the hippogriffs didn’t have to retreat to in between their mountain shroud anymore.
 
Another reason for building lowland settlements was certainly because many hippogriffs didn’t want to let go of their lives as seaponies. But the old settlement uphill was too far away from the shore, and the hippogriffs always had to fly up and down half the mountain. Good thing they’ve got wings, they would have had to use those narrow stairs instead (Silverstream probably does use them whenever possible).  

 
Population growth may of course be another reason. I mean, they’ve even settled on a nearby island. (“A bridge? We’ve got wings, and we can swim!”)
 
The land bridge is definitely artificial, but I don’t think its construction was that easy. The water isn’t that shallow in this area; remember there’s still Seaquestria down there. My guess is that it was a combined effort involving dragons and molten lava with a bit of unicorn magic to keep it from cooling during the transport. (They may have used the same technique to restore the Well of Shade if they did.)
 
As for the railway line, it may be a new extension of the line to the Hayseed Swamp which leads down the east coast.  
 
It clearly didn’t go all the way to the southern coast by the time of the film, otherwise the Mane Six wouldn’t have had to cross the Bone-Dry Desert. They simply could have taken the train (unless the Storm King’s attack had brought Equestria’s railway system to a halt).
 
Also, the film didn’t show the land right opposite of Mount Aris. The Mane Six end up on Basalt Beach instead. According to the film, Mount Aris lies west or southwest of Basalt Beach and not too unlikely opposite an area that has been inhabited by ponies by the time of the film already. It may be the Equestrian version of Ireland, for all we know, a province called Shireland. Needless to say that the Shirish ponies profited from the new Mount Aris Extension. Before it was built, Shirish pegasi must have shuttled visitors to Mount Aris and back in carriages (we don’t know how good hippogriffs are at pulling vehicles in the air, but it’s safe to assume that they didn’t have any vehicles on wheels at all since Mount Aris’ topography makes their use difficult to say the least).
 
Klugetown won’t be connected to the railway network as long as it stays the lawless place that it currently is. Besides, it’s of no use for Canterlot, and lying in the middle of the desert, it isn’t any danger either, so there’s no need to take care of it yet.

@Frustration in Excelsis  
Well, they may had also hired foreign pony workers (including that hardhat “alicorn”) to assist in the reconstruction project of their ghost town

This brief shot gave a lot of information about the state of the hippogriffs and Mount Aris. Just from this brief pan we can see a great many things that were either skipped in the movie or built later in-universe:
 
Firstly, there seems to be some substantial settlement along the base of the mountain itself, rather than just the city on the summit. Either that just wasn’t visible in the movie or – I’m leaning more towards the second option – built afterwards. Perhaps the population grew enough during the exile that some extra houses were needed, or perhaps that part was built to accommodate and service the new traffic between the island and the mainland?
 
On the note of traffic, there’s the land bridge. That’s definitely new, and I agree with @Scintilla Aquila – it’s too thin, straight and regular to be natural. That definitely looks like something someone built. Since Mount Aris was an island in the movie, it’d have to have been built afterwards.
 
Thirdly, there are the houses and farms around the coast near Mount Aris itself. There’s no way to tell if they were built recently or if they’re older things reclaimed after the Storm King’s defeat, but they definitely weren’t present in the movie.
 
Regardless of the specifics, it’s clear that the hippogriff/seapony nation went through a lot of very impressive building and rebuilding since the movie.

That village road’s much more steeper than Baldwin Street of New Zealand!
 
If I knew the town was gonna be that steep, I would’ve brought my portaledges!  

That they built a land bridge to Mt. Areas is actually the least impressive thing about this. There’s a large dessert and a not so large swamp/forest between Equestria and Mt. Areas. Even if they started expanding their railroad tracks from Farthest Reaches, they still managed to finish it in an impressive amount of time considering the harsh environment.
 
It also makes me wonder, is Klugetown now connected to the Equestria railroad system? Or did the ponies (wisely) decided to avoid that city like the plague.

@Background Pony Number 17  
That’s not exactly inconsistent with the very thin, unnatural-looking strip of land on which the railroad is built. It could still have been an island during the movie and then joined by this artificial land bridge when people decided a railroad was in order.

Not to scale.

“Okay, we did the balloon last episode. So this time the ponies take the train to Mt. Aris.”
 
“But according to the movie, Mt. Aris is an island.”
 
“Details, details…”