>>9659759It might be the paint more than the clearcoat. Tamiya acrylics have a tendency to end up extremely matte, to the point where it makes them significantly lighter than they'd otherwise be. See this propeller spinner for example, painted XF-7 flat red. The lower end is as-painted, and nearly pink in appearance. The upper side has been given a temporary coat of plain old water, and shows the proper red colour.
So when you clear-coated your model you may have removed this excess bit of lightness from the paint, and I guess the darker areas may show this better since the difference between the "real" colour and the lightening surface was greater there.
If this guess of mine is correct then there's no practical way of directly undoing it. If you want it lighter and with less contrast then either mix up some lightish hue of paint and spray on with a suitable amount of translucency, or adjust your weathering and filters to do it instead.