The baseline guidelines might both still apply though, let me throw this interpretation out there. Either way, you should ask for clarification on your proposed path before submitting if possible.
1. Model the existing as-is per the reference that you noted. Seems straightforward.
2. Whole-building totals might still be required to match the 40% and 5%, unless superseded by #1. This seems to be the point of discussion with the reviewer.
In that case the baseline total glazing for the existing portion would be modeled as existing. The new construction baseline would have any remainder of glazing area up to 40%. It sounded like you would be below 40% total, so model as you did before with the basline = proposed.
For skylights the existing building "consumes" more than 5% of the whole project, therefore the skylight area would be capped at whatever the actual percentage is based on the existing. The baseline would not have skylights in the new construction unless they were required to be added by some other part of the code or local requirements in order to meeet the 5% requirement. This could benefit you if the project is adding photocell control of the lighting in the new addition in conjunction with the skylights.
G1.3 is tricky since there is also a new portion to the project that can still impact the overall percentages, even if the existing portion is modeled as-is. And none of the complex is excluded from the renovation, although the envelope may not be changing. Assuming that lighting, HVAC, and interiors are being renovated in the existing warehouse? Otherwise your LEED project boundary should only be the new addition.
David S. Eldridge, Jr., P.E., LEED AP BD+C, BEMP, BEAP, HBDP