The main intent of the MPR and supplemental guidance requirements regarding additions is to discourage the LEED certification of one part of a building that is not clearly separate from the rest of the building that is not being certified. That's not the case here, since both are getting certified, so you just need to figure out what's a reasonable approach.

The question is whether that addition should be added into the original LEED submission as part of that project and included in that one LEED submission or treated as a separate project for a separate LEED award. It may depend on how far along is the design review for the first phase. You'll probably want to contact the GBCI and explain the situation and your timeline to see if they advise combining the two or registering them separately. If you have different design team members, contractors, HVAC systems or specs for the addition, it might be easier in the long run to treat them as separate projects, but if it's mostly the same, see if you can combine them into one.

If you need to treat it as a separate project, you'll probably want to register it as a "block" when you register in LEEDOnline so it can be associated with the first project and thus reviewed by the same review team.

Also check the MPR Supplemental Guidance document pages 15 - 17 for how to deal with the site area and LEED boundary in phased projects.