That is not a hinting problem. Simply the overlap is causing this.
try using corner or cap components instead of real components. That will result in a single path and avoid that issue. and is easier to keep in sync.
Yes. It had nothing to do with hinting, but quite the opposite: with antialiasing. Variable fonts keep their overlaps and each shape has semitransparent border pixels for making it appear smoother and staying closer to the original shape. And if a part of the edge is shared by two shapes, the antialiasing pixels will add up their opacity.