Running Wikibase locally, I can generate results via curl:

curl http://localhost:8989/bigdata/sparql?SELECT%20DISTINCT%3Fp%20WHERE%20%7B%20%3Fs%20%3Fp%20%3Fo%20%7D

But trying to query the same endpoint with wikidata-taxonomy returns data from Wikidata instead:

node wdtaxonomy.js Q3 --sparql-endpoint http://localhost:8989/bigdata/sparql 
life (Q3) •188 ↑↑↑
├──extraterrestrial life (Q181508) •81 ×1 ↑
│  ├──life on Mars (Q601319) •34 ×1
│  ├──Martian (Q913850) •25 ×4
│  ├──Life on Titan (Q2591050) •15
│  └──extraterrestrial intelligence (Q15107669) •7
├──personal life (Q2867027) •20
└──human life (Q19771042) •3

I get the same result if I install wikidata-taxonomy globally with npm install -g

It's late night so I'll toss a theory: does it implicitly depend on properties such as P279 existing in the target endpoint, and it falls back to Wikidata if the query to the specified endpoint doesn't return the expected data?