At eTool, our best practice recommendation is to get both your Reference and Proposed designs certified. There are a number of benefits for this.
1) You’ll be able to generate reports from any certified design without watermarks;
2) Getting your study reviewed externally is an additional means to catch big errors, if any;
3) The certified design is ‘locked’ which is actually a way to secure the study so that study audiences can feel confident that the study has not been altered (intentionally or unintentionally) after that point.
4) Some rating systems award points for getting your LCA externally reviewed.
Nonetheless, it is not an eTool requirement to have both your designs certified if you do not wish to take advantage of the benefits listed above.
I hope that answers your question!