I see there is code in the AddWork and AddCoveredWork activities that get the work object prefix from the application rule and append a - if one is not present. It seems possible there could be other code dependent on that structure but I am not sure.
If it is simple prefix change, then you can do changes in Cases&Data.
Otherwise, the following steps can be followed to change the Work ID prefix without overriding the Work-GenerateID activity if it has only Prefix change.
1) In the Cases&Data tab of the application rule, make prefix id as empty.
2) change .pyWorkIDPrefix value whatever you want to change in pyDefault data transform for that case type.