Yeah that's a fair point. The purpose of the application isn't to provide fine-grained control over plugins etc yet.. However, I do intend to add settings configuration for some plugins. Which plugins I'll do this for depends on their popularity and whether they have WP-CLI compatibility built in.

In the meantime I may see if I can also embed the WP admin page so the user has quick access if they want to change anything.

Thanks for your feedback!