WordPress Mobile Pack is mostly suitable for content creators such as blogger, digital newspapers or magazines. It currently supports blog posts/articles and pages who want to repurpose their existing content into a progressive web application. Since it has been shown that progressive web applications greatly increase conversion rates (https://developers.google.com/web/showcase/) we've included in our roadmap to implement support for e-commerce business (get in touch if you want to know more).
The _progressive web apps _created by WordPress Mobile Pack are independent of your WordPress desktop theme. We use the WordPress REST API to take the content from your WordPress and we display it in a client-side rendered app, which is in fact a single-page application.
By doing it like this you also have the option (not the obligation) to package it into a hybrid application and submit it to App Stores (Google Play, Apple Store).
There are almost 50,000 plugins on WordPress.org repository. The objective answer is that it depends.
Because we're using WordPress REST API to take the content from your WordPress, the question becomes: is your plugin compatible with the REST API? If the answer is YES, than it should also be compatible with WordPress Mobile Pack.
Please notice that many plugins will only make sense in the desktop theme. Plugins implementing major features such as WooCommerce don't work with WordPress Mobile Pack out-of-the-box. We are already working on an extension to make WordPress Mobile Pack compatible with WooCommerce.
If your WordPress site requires a plugin and it is not compatible with WordPress Mobile Pack, please reach out at firstname.lastname@example.org.