The following can be used as a workaround:
1. Create a custom attribute on the "Benefit Plan Detail" object, say, "Benefit Variance Custom"
2. Display this custom attribute in the "Benefit Plan Detail - List" view
3. Take away the OOTB, "Benefit Variance" attribute from the above mentioned view
4. This will provide the users the ability to manually enter the Benefit variance
5. Further, a process can be developed to make the variance calculation, and lock the field for user input.