Different Mappings per namespace, get overwritten due to embedded-git-config.json

Take an enterprise solution consisting of 2 interoperability production, running in two different namespaces., and one git repository, (called for argument's sake - "MySolution").

The IRIS instance defines a git initialise root folder: c:\MySolution.
The IRIS instance defines namespaces APPA and APPB where these productions are developed, and I want code edited/saved in each namespace to go to a namespace appropriate sub-folder.

The export mappings as therefore defined in Settings UI say,
- for APPA, that CLS files export to /APPA/src/cls, INC to /APPA/src/inc, etc.
- for APPB, that CLS files export to /APPB/src/cls, INC to /APPB/src/inc, etc. - you get he idea...

This works fine - initially...., but changing these settings via the UI creates an export file: embedded-git-config.json in the ROOT work folder, with the most recently updated namespace values (which could be APPA or APPB), and re-entering into the other namespace's Settings UI, loads and *overwrites* these previously defined namespace-specific mappings.

What is the use of this embedded-git-config.json ? Am I forced to a one-to-one mapping of GIT Repository to Namespace ?