I migrated all my DTM properties with the unchecking status of the two checkboxes. the advantage I see here is, the developer can build and test the launch script before pushing it into the production. we have an option to test in QA and Stage environment and when everything is ready I used to publish and share the production script path to the business people to configure in their respective applications.
The other checkbox which is "disable property after upgrade", once the testing and everything is completed and working it on the production then you can go and disable the property manually in the DTM.
With the above approach, I did not see any issues.
When you select checkboxes and publish launch script you do not need to share .js script to the business people to configure in their applications, the system will automatically replace the existing DTM script with the launch script.
The second check automatically disables the property in the DTM.