The way "time allowance" interacts with the "completion date" is currently rather confusing.
There is another (unfortunately rather long) thread that goes into detail on how the time allowance exception works here:
https://totara.community/mod/forum/discuss.php?d=16928
The upshot is that the "time allowance" option in the courseset section actually means "Minimum time required a user should have to complete this set".
Typically you would set this to something quite short, then use the completion settings on the assignment tab to set when users should actually complete it by.
Simon