This seems to be a bug (or unexpected behaviour at least) in Atom – IIUC Open File does the equivalent of atom filename in the terminal, which has the following behaviour:
~ atom --help
Atom Editor v1.19.0-beta2
Usage: atom [options] [path ...]
One or more paths to files or folders may be specified. If there is an
existing Atom window that contains all of the given folders, the paths
will be opened in that window. Otherwise, they will be opened in a new
window.
This means that you can’t open files in one folder/project in two different instances of Atom with Open File; atom -n filename does work though.