Map note icons - but not adornments or the title part of containers/agents or adornments - can use transparency. The transparency allows background items to show through where notes overlap.
Note transparency is set via the $Opacity attribute, with 100 (default) being opaque and 0 being totally transparent. Unless the $Border is also set to 0, a note always retains a border regardless of transparency.
Transparency is effected within the normal stacking order of a map. Thus if transparent note A overlaps opaque B, if B has the higher $OutlineOrder, B will simply overlap A. If the $OutlineOrder is reversed A will both overlap B and B will be visible within the overlap.
Adornments, by default, already have a built-in fixed level of transparency.
As of v5.10.2, the opacity of a note's title and subtitle can be set separately from overall note opacity via $TitleOpacity and $SubtitleOpacity. Be aware that $Opacity still trumps the latter two attributes - if their values are greater than that of $Opacity, the latter value is used for all. Thus if $Opacity is 100, $TitleOpacity my be 50 - half that of the overall note. But, if $Opacity is 50, $TitleOpacity my be 100 the title is drawn at 50% opacity.
In short, the latter ends up being generally what might be expected. It does preclude having a 'invisible' note with a visible title. To do the latter, set $Border to zero and $Pattern to "none" and $Color to the parent container's $MapBackgroundColor.