Well, the game creators are trying to produce a 'scary feeling' to the place.
Like, the Goldenrod Underground is home to, according to most, scary-strong trainers, and that they should be challenged with caution.
Same with the Ruins of Alph. This is home to a bunch of Unown that could suddenly pry themselves out of a wall and attack you with their powers.
The music directors do this normally. If you hadn't notice, Azalea Town and Blackthorn City share the same theme song as well. Of course, that music is neutral and doesn't produce no feelings really. xD
Hope I helped. :)