When to use alignment? Always?
Not always! Use alignment only when necessary and when you made sure that the quality is to your expectations.
If you create a Beebox project for the purpose of aligning a lot of files, you would of course enable alignment by default (no need to create instructions files).
If you integrate the Beebox with a CMS you should use instructions files so that the CMS tells the Beebox exactly which translated content needs to be aligned: The content that was actually edited or annotated by the user.
When and how does the Beebox align?
...