They're proper areas in CITY.TXT. See for example:
[Area 37] ; Special Encounter Cafe of Broken Dreams
area_name=Special Cafe
world_pos=120,350
start_state=Off
lock_state=Off
size=Small
townmap_art_idx=-1
townmap_label_art_idx=-1
entrance_0=On,345,230,Special Cafe Encounter,-1,-1,0
[Area...