As Indesign & Illustrator unfortunately is doing right now:
If the overprinted area contains a smaller amount of the same base colour (c/m/y/k) than the overprinted area, the overprint function mutates into a kind of cut-out function:
in which case Adobe replaces the area of the cutoff area with the lower color value of the area to be overprinted.

Example 1
Area below to be overprinted (cmyk): 20/0/100/0
Area at the top that is to overprint (cmyk): 40/0/0/0
A.) Current result cut surface: 40/0/100/0 (okay)
B.) Correct result cut surface: 40/0/100/0
or C.) alternative result* cut surface: 60/0/100/0
(*where the value is added until it reaches max. 100% of the color value)

Example 2
Area below to be overprinted (cmyk): 80/0/100/0
Area at the top that is to overprint (cmyk): 40/0/0/0
Current result cut surface: 40/0/100/0

Example 3
Area below to be overprinted (cmyk): 80/0/100/0
Area at the top that is to overprint (cmyk): 40/0/0/10
Current result cut surface: 40/0/100/10