I created Buffer (with Vector, Geoprocessing Tools) with 500 M distance from a point in the map (let's say Point A). I made another point (Point B) and it is not inside the 500 m Buffer. The Distance matrix tool shows that the points are separated about 413 M from each other. I noticed that this difference comes (using the Measure Line tool), because the buffer has Cartesian distance, yet the distance in Distance Matrix shows the ellipsoidal distance values.
How to either make the buffer in ellipsoidal distance, or let the distance matrix shows Cartesian distance?
Note: The Cartesian distance of point A and B is about 661 Meters for each other.
Answer
Buffer tool uses the CRS of the layer.
We can't have an "ellipsoidal distances" projection.
So, if you want to draw buffers with the ellipsoidal distance in QGIS, the most similar that you can do is project the layer to a CRS that do not deform the distances so much in your work area.
Also, that is the best practice.
Distance matrix tool uses the ellipsoid definition of the project to make measurements.
In Project menu, Porperties, General tab, Measurements section, you will find the ellipsoid definition for the project and the units used for ellipsoidal measurements.
But you can define there the strange "None / Planimetric" ellipsoid, which turns all ellipsoidal measurement tools to planimetric.
So, you can measure planimetric (Cartesian based in the CRS of the layer) distances in Distance matrix tool.
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