When to use the Flag module versus a boolean field? In terms of performance, maintenance, and future expansion/migration, what are the advantages and disadvantages of using the Flag module versus a boolean field?

In my case I would use the module to mark articles in a newspaper website that will be featured on the front page.
For this particular use case, you could go with the field. There is no need to install a contrib module for something that a field can do fine.

Flags create a new entity for each new flag you create. This adds an extra layer of complexity when you are need to migrate or deploy. 

It would make sense to use flags, if for example, you wished that your each of your users could mark this article (eg mark it as favorite)

Drupal also offers the 'promote to front page' functionality that you could use.