It is currently not possible to pass explicit credentials directly into fileDatastore. Datastore retrieves the credentials in the same way as the Amazon command line interface, either from environment variables or from the Configuration and Credential pair of files as described by Amazon.
With that said, different processes can have their own credentials. The setenv function in MATLAB affects only the MATLAB process itself, as well as any application launched by calling the system function in MATLAB. It is safe to use setenv in MATLAB, all other applications outside of MATLAB will continue to see their own copy of the environment variables and use their own credentials.