The JSONs in that part of the OpenStudio Standards repo are where that recommended measure generates the geometry of the prototype models from. Using the 3-year-old OSM files in that part of the standards gem repo is better than working from those very old IDFs but you’re probably still loosing some information compared to actually re-generating the prototype models using the measure. So that is what I would still recommend doing.
Your LargeOffice prototype model is correct. That DoE reference building uses multipliers to represent the repeated stories so that the simulation does not take too long to run.
It looks like the errors that you are encountering are because you are working from the 3-year-old OSM. When I generate the LargeOffice using the measure in OpenStudio Application 1.6, I get an OSM that I have no issues simulating with the latest LBT plugin that used OpenStudio 3.6:
LargeOffice.osm (1.2 MB)
simulate_osm.gh (11.5 KB)
So just use the recommended measure and you’ll be fine.