SLB does indeed automatically activate image links in posts, pages, etc. without any need for manual coding required. If you want to manually set up a lightbox for each link in every post, then this plugin is not for you.
Although, it is strange to say that it doesn’t fit in with how WordPress works, as automatic activation is common for many lightbox plugins, including WordPress’ own Jetpack lightbox.
Even then, SLB is not all or nothing, as it provides options to control enabling SLB for different content areas such as posts, pages, widgets, and menus, as well different types of requests such as the home page, archive pages, single posts/pages, etc. (perhaps you missed these settings?). Beyond that, excluding specific image links from being displayed in a lightbox is possible with a simple shortcode, which is very much in line with standard WordPress functionality.
Finally, SLB is completely free for all users and supports all plugins that use WordPress’ standard content areas. The main plugin supports WordPress=specific content areas to keep it as lean as possible and avoid unnecessary bloat. Support for plugin-specific content areas is provided via extensions for those who want it. As SLB is open-source, you can view the code to see that no functionality is “blocked”.
WooCommerce uses some native WordPress content areas, and SLB is fully supported in these content areas. However, WooCommerce also uses some non-standard content areas, so support for these content areas and other functionality is provided via an extension.
