After a bit of investigation, it seems that the crucial difference is the setOpaque(false) 'ness that is problematic. When the toplevel window is opaque, no mouseclicks fall through, no matter how much I bombard it. The same goes for a component in modal state.
When the top level window and the modal component are non-opaque, it happens that mouseclicks fall through them - regardless of the painted content or child components.
An interesting finding though, is that when a portion of the window is completely transparent (i.e. nothing is drawn, and likewise for any child components in front), the clicks fall through every time. It seems like the more transparent, the greater possibility of mouseclicks falling through. It is not directly proportional though, because when the window has a completely opaque background (drawn, not setOpaque(true)'ed), then it still happens that clicks fall through.
What do you make of this…?