Why does it make sense that this story takes place in a cantonment?

A cantonment is a military base in India.  The Kipling Society notes that the Segowlee Cantonment is a fictitious location; however, a cantonment is a real place where soldiers live and train.  A cantonment is a place for warriors.    
It makes sense that this story happens in a place where warriors live because Rikki-tikki is a warrior.  He may not be fighting humans, and he may not have human weapons of war, but that doesn't mean Rikki-tikki isn't a warrior with warrior weapons.  He's very quick, and has teeth that are capable of stabbing flesh for the killing blow.  Rikki-tikki is asked to put his warrior skills into practice during this story too.  He kills three deadly snakes over the course of the short story.  For a children's story, the body count is fairly high.  
The opening paragraph of the story also helps sell the cantonment setting.  

This is the story of the great war that Rikkitikki-tavi fought single-handed. . . 

Readers are introduced to a character fighting a war.  Active combat soldiers live in military bases.  Rikki-tikki is an active warrior in this story, and he is housed in a cantonment.  
http://www.kiplingsociety.co.uk/rg_rikkitikki_notes.htm