I sliced your project using 0.4 and 0.5 line widths and the extrusion amounts for the wall line scaled as expected.
Here's the 0.4mm line width extruding at 0.050 mm/mm rate (which is correct if you do the calculation)
And here's the 0.5mm line width extruding at 0.062 mm/mm (which is also correct)
I don't think Cura is causing the problem you observe. Hope this helps.
Here's the 3mf that should have all my settings if it helps
PI3_20mm plain cube.3mf
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