Take look at your example closely... Both are correct, only difference is that dxf41 and dxf42 represent angles in radians of parent circle used to construct elliptical arc with projection of main ellipse axis from main circle angles back to ellipse... On the other hand (vla-put-(start)(end)angle) function takes explicitly that angle from parent circle and doesn't project it back to ellipse - it just extends them to elliptical arc...
Attached your example as *.dwg...