No,When Subject based registration is active then the corresponding subject amount is calculated only.We don’t have provisions to set handling charges.
But you can always do that by adding that amount in the subjects itself.
Cost for Estimated cost of registration
Subject 1 $200
Subject 2 $200
Subjects Opted for Estimated cost of registration
Subject 1 $225
Subject 2 $225
The requirement of case 1 can be met by revising the subject amount as case 2.
Note:-In such a case one can also use the instant fee collection in the fees section.