In v5.90 the same problem remains.
Item mix behavior: Items always replace earlier items
Auto-crossfade - disabled
Trim content behind media items when editing - disabled
I tried to use the custom Action for Mouse Modifier "Media Item: left click":
1) Item: Unselect all items
2) Item: Select item under mouse cursor
But when I click on the enclosed item, other layers behind it select, too.
It seems, that z-index of the overlapping items needs to be fixed.