I did this in 2009 for some office project handover, and it remains fundamentally correct today (probably the “Undo” warning would not be necessary, but I haven't checked). If there are not that many modules or module instances of any kind (unit, envelope, kitchens, furniture, whatever), there may be no need for 'depot' files.
You can place (if not copy-pasting from the depot) your building story module hotlinks on the site file, and then elevate them individually into position. Because each building can have its own story structure (not only different starting levels, but also different story heights), you will most likely want to define a starting level as ±0 for each (you can change its Reference Level as many times as you want), use the building files for cutting building sections-producing building schedules-etc., and use the site file for generating site sections-etc. only.
With multi-file projects, updates of the pln and even worse BIMcloud file become a pain, so I think it is still best to publish to PMK, and bring those PMKs into a layout book pln. So on one hand you decide on each model file when its PMKs will get published, and on the other you decide on the layout book file when you will update those links (and module links on the model files, and PMK links on the layout file, will only show 'modified' when you have republished them, as opposed to each time you modify the model file).
You only need to publish into each module the content you will be wanting to show on the higher level file (you control that with the layer combination you use for publishing those modules); for example, you may not need room zone stamps, etc., on the site file.
https://www.dropbox.com/s/lyyimdg0wtc5rmx/Wyndham_file_structure.pdf?dl=0
