You can refer to the pipelines described in this tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/Workflows#Statistics:_Group_analysis.2C_between_subjects-1
I am not sure how to retrieve the scores (generated from the ROIs or scouts) so that I can use them in a different statistical software.
Please post screen captures of the files you have (database explorer + display of these files), describe the measure you would like to extract from them.
Please create a different thread, as this is not related to the initial question posted here.
Lastly, is it ok if I use the source files and do the comparison using SPM 12 or should I go with permutation/parametric test of these source files using brainstorm?
This is up to you to decide what kind of analysis you want to perform on your data.
The documentation of the Brainstorm statistics:
https://neuroimage.usc.edu/brainstorm/Tutorials/Statistics
The documentation to export data to SPM as surface or volumes:
https://neuroimage.usc.edu/brainstorm/ExportSpm8
https://neuroimage.usc.edu/brainstorm/ExportSpm12