I should say, for the input data, each timeframe output for each RCP is stored in a NetCDF file - but that's overall. Each model deals with a single NetCDF input file; the SBD tool runs on it to select the appropriate raster data, and copy it out to individual raster files. Perhaps it's easiest to show in the non-interated form:
Each of the individual rows runs on each dimensional value, then merges the layers to create the ensemble, clips and projects out as appropriate.
This is a separate model, but identical template (the broken nature of the far right is unrelated to this issue, that's just a question of file paths changing between computers and isn't related to the OP in this case).
It's the left portion that we are obviously trying to iterate. The "For" operator seemed the appropriate one from the material that I read regarding it, since what is being selected are individual dimensions within a multidimensional dataset, but if a different iterator is more appropriate, I'm open to considering that as well.