You could create a new data card and save it into that folder where configurations are being used. On this data card, you would need to create new variables that aren't mandatory. I'm not sure there are any ways around this. When you don't have 'Updates all configurations' checked and the field is Mandatory (I'm assuming you've set this at the Variable level) then it has to have a value when you go to save the card info.
The drawback to using a unique card and unique variables is your searching is now affected since you have all new variables that need to be included in searches.
Maybe someone else has a better idea.
We don't use mandatory datacard fields at all because they cause all kinds of problems. Besides the issues that you mentioned, it is also not possible to enable the mandatory flag to an existing variable if files are already in the vault with empty values.
Fortunately, there are other ways to make a field 'mandatory':
1. Set the minimum and/or maximum text length for datacard fields
2. Use Dispatch to check variable values during check in or state change. This way you can easily skip the @-config.
3. Use workflow conditions to block transitions if variable values don't meet conditions
Hope this helps,