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Don't ask me why but if you add this two lines it works om my computer

   // Apply TPS
    transpose(pointmatrix1, pointmatrix1); // ADD
    transpose(testpoints, testpoints); // ADD
    Ptr<ThinPlateSplineShapeTransformer> mytps = createThinPlateSplineShapeTransformer(0);
    mytps->estimateTransformation(pointmatrix1, pointmatrix1, good_matches); // Using same pointmatrix nothing should change in res
    mytps->applyTransformation(testpointsmat, resmat);

Now There is something strange in source code here

Don't ask me why but if you add this two lines it works om my computer

   // Apply TPS
    transpose(pointmatrix1, pointmatrix1); // ADD
    transpose(testpoints, testpoints); // ADD
    Ptr<ThinPlateSplineShapeTransformer> mytps = createThinPlateSplineShapeTransformer(0);
    mytps->estimateTransformation(pointmatrix1, pointmatrix1, good_matches); // Using same pointmatrix nothing should change in res
    mytps->applyTransformation(testpointsmat, resmat);

Now There is something strange in source code here

Don't ask me why but if you add this two lines it works om my computer

   // Apply TPS
    transpose(pointmatrix1, pointmatrix1); // ADD
    transpose(testpoints, testpoints); // ADD
    Ptr<ThinPlateSplineShapeTransformer> mytps = createThinPlateSplineShapeTransformer(0);
    mytps->estimateTransformation(pointmatrix1, pointmatrix1, good_matches); // Using same pointmatrix nothing should change in res
    mytps->applyTransformation(testpointsmat, resmat);

Now There is something strange in source code here why cols and not rows

Don't ask me why but if you add this two lines it works om my computer

   // Apply TPS
    transpose(pointmatrix1, pointmatrix1); // ADD
    transpose(testpoints, testpoints); // ADD
    Ptr<ThinPlateSplineShapeTransformer> mytps = createThinPlateSplineShapeTransformer(0);
    mytps->estimateTransformation(pointmatrix1, pointmatrix1, good_matches); // Using same pointmatrix nothing should change in res
    mytps->applyTransformation(testpointsmat, resmat);

Now There is something strange in source code here why cols and not rows

Following remarks of @juanmanpr That's can be done too

   // Apply TPS
    Ptr<ThinPlateSplineShapeTransformer> mytps = createThinPlateSplineShapeTransformer(0);
    mytps->estimateTransformation(points1, points1, good_matches); // Using same pointmatrix nothing should change in res
    mytps->applyTransformation(testpointsmat, resmat);

that's better thanks @juanmanpr