In this commit (refs #1404) , the starting phase, disabled techs, disabled templates and starting entities garrisoned were added to the JSON part of the map.

This seems right for all properties that apply to players.
But the Garrison property contains entity IDs (thus is incompatible with random map scripts) and would better fit to the other places that hold the Entity information, i.e. XML <Entity> list IMO.
(See rP16279 for a map using the property.)

CXMLReader::ReadEntities of MapReader.cpp loads the entities and it sets all properties of the other simulation components as well, so it could set this one too.
One might argue that the C++ code only sets the properties that are shared by almost all (i.e. foremost gaia and actor) entities while the Garrison and other simulation properties should not be present in C++ to keep the engine split from the public mod.
On the other hand we likely want to make the Garrison property a setting in Atlas.