Each type of the folded-code-marker overrides the style of the current line, not just the one for regions. This is visible if you have a separate highlight style for the line with a caret - then the highlight style is replaced by the one for the marker. See the attachment — this is what the marker looks like for a folded comment and any other folded code fragment for me (zoomed twice, line 2059).
I think this can be considered a bug, because if the background for the folded marker is not set, the marker is rendered on top of the line, ignoring the current line style. If any of you use trunk, please check if the problem occurs in the circumstances I described.