Brendan,
I suppose there is a trade off between the options of all buildings in one
file and individual models.
The all buildings in one file option treats other buildings as shading
objects in E+ and as wind shields & shading in design builder, but does not
allow for the use of zone multipliers.

The individual model option allows for zone multipliers and this means
shorter simulation run time.

So I guess it depends on your use; if you want fast run time, single models
are best but if you want to model the geographical features more accurately
than multi model would be best. If you set the project up in DB, then
export to E+ than the other models will be shading objects, for existing
buildings this is what I like to do.
The logic is that for existing buildings the owners are likely to make
changes to individual zones, so use of zone multipliers may not provide
useful info.

hope this helps and best of regards-
*Jeremiah D. Crossett*