Hi,
The default choice of your custom field should be a value with just a title like for example "please select something" and no value data.
That way, when you save a variant for something else you want to modify, the system will save an empty value in the field and the characteristic system will continue to use the main product value instead of the variant value.
Alternatively, you could also create a mass action which would be triggered after the product update with a filter to apply it only to the variants and an "update the values" action to set an empty value to the field. That way, regardless of how you configure the field or what you select in that field in the variants, the data of the field for the variants will always be empty.
So that's two solutions for you