Current Thrinacia Atlas WordPress plugin is a wrapper around Thrinacia Web UI. It is not fully integrated WordPress solution.
The plugin ensures Web UI can easily be activated and run from the predefined website path. It also allows your WordPress website to still function as normal but it reserves its own pre-configured path for Thrinacia Atlas Web UI.
All Web UI files are shipped with the plugin and can be customized as needed. Similar custom development and bundling/build process can be used to build the Web UI for the WordPress plugin. That process is described here: https://www.thrinacia.com/faq/post/how-can-i-make-custom-modifications-to-thrinacia-atlas-wordpress-plugin
Note that Thrinacia Atlas WordPress plugin is not fully integrated into WordPress, so it works in a same way as Web UI. Communication is done with Atlas REST API for your instance, menus will likely need to be maintained on both WordPress and Web UI side and any theming needs to be implemented in the actual Web UI to follow the theme of your website.
Theming changes for the WordPress plugin Web UI can be done by changing AngularJS views/partials/controllers or by adjusting custom CSS in a same manner as customizing the standalone Web UI. That process is described here: https://www.thrinacia.com/blog/post/new-development-workflow