I ended up creating this npm CLI tool auto-apm to do this so it benefits everybody.
npm install -g auto-apm
Only install missing Atom packages and skip installed ones.
Usage: auto-apm [options]
-h, --help output usage information
-i, --install [pkg1,pkg2,pkg3,...] a list of packages to install
-p, --packages [packages_file.json] a .json file containing a list of packages to install.
-i is specified, it must be followed by a list of packages to install, seperated by
auto-apm -i zen,minimap
-p is specified, it must be followed by a JSON file containing a list of packages to
['minimap', 'zen', 'autoflow']
packages_file.json is omitted, it looks for
When it runs, it looks like this: