Can I include some manual effort in creating an otherwise automated research prototype tool?
You can do that.  I have seen other papers that generate dummy classes like that (e.g., Klee).  How useful this will be may depend on how much effort it takes to write those dummy classes and how many are needed.
What matters is less the name (automated vs manual) and more that you describe clearly in your paper what its advantages and drawbacks are.  Usually it is valuable to compare to prior papers.  Can you demonstrate that your method is easier to apply than prior work?  Maybe because it requires less manual work?  If so, you may be in business.