One way to approach this could be to register the project with the square footage and LEED boundary defined as per Phase 1 and hold off on submitting for any review until you know the status of phase 2. The certification review fees are based on project sf, so once you decide to submit for review it could be hard to then change the scope of the project.

I think it would be reasonable in the future to adjust the project data such as area, FTE, and LEED boundary to include the phase 2 work and submit it as a single project as long as you have properly documented all the credits to include the work done for both phases. For many of the MR and EQ credits it won't change much if you're using building standard specs; the materials cost totals tracked for MR and VOC lists for EQc4 credits will expand. It's a whole lot easier if the same GC and Commissioning agent does both phases, and if the systems are consistent throughout the building.