Then don’t do it. 
I am (currently) running Netlify Analytics along with Counter on a couple of sites. And yes, they show different results. But then so has Google Analytics compared to Mixpanel or Heap Analytics (and others) when I have used them in the past.
Another threads you might find interesting (if you haven’t already read them): Over 100x more views in Netlify Analytics than Google Analytics?, Netlify Analytics showing 10x more results than GA, or search netlify-analytics.
You may get more answers from the above linked threads. If not, a Support Engineer might provide you with some more specific insights.