The IOS Native plugin is shipped with a built-in IOS Deploy plugin inside. The idea is, that you do not have to do any manual modification with XCode project once the application is built. And to achieve it we have own SDK, that is based on Unity PBXProject  API. So why not give you nice visual UI to set up XCode various XCode project settings.

Apart from a wrapper around PBXProject  API, the IOS Deploy plugin provides features that not yet available with PBXProject.

However, you do not have to use it. IOS Native plugin will use it internally and will make all the necessary modification to make sure you can you can use "Build & Run" and have not issued with "Cloud Build"

Open the XCode tab of plugin editor settings to find see all the variety of features. You will find a more detailed description of the plugin XCode API & features inside XCode documentation Section.