Changes in SMath 0.97.5327:
Opening and closing separators of an area region do not know anything about each other, just as with opening and closing parens.
Therefore, now you cannot create overlapping area regions any more, instead you create nested area regions. This logic is straightforward and might solve the original request.
Opening and closing separators are matched by nesting level and proximity. Deleting any area separator now also deletes the matching one, which was ioan's request 1
Color changes to any separator of an expanded area just affect this separator. The matching separator and the contents inside are not affected.
Color changes to a collapsed area region affect everyting (separators and contents.
Only remaining issue of this request is saving the contents of an area region to a file. Current workaround would be to copy the region (possibly collapsed) to a new file.