I don’t know. This would be a general PWA question and not specific to the PWA plugin for WordPress. You could ask the question on Stack Overflow: https://stackoverflow.com/questions/tagged/progressive-web-apps
Nevertheless, disabling the context menu is not a normal aspect of PWAs as far as I know. If the context menu is showing on your site when you browse to it, the same context menu would show when the user interacts with your site installed as an app. Your site should behave the same in both cases.
In other words, PWAs are not “native” apps.