Unity3D will not contains folders in the Plugins/iOS to Xcode project. In fact Unity3D will only auto merge source file and .a library for you, as described by Unity3D's doc:
Automated plugin integration Unity iOS supports automated plugin
integration in a limited way. All files with extensions
.a,.m,.mm,.c,.cpp located in the Assets/Plugins/iOS folder will be
merged into the generated Xcode project automatically. However,
merging is done by symlinking files from Assets/Plugins/iOS to the
final destination, which might affect some workflows. The .h files are
not included in the Xcode project tree, but they appear on the
destination file system, thus allowing compilation of .m/.mm/.c/.cpp
files.
Note: subfolders are currently not supported.
But you can use the PostprocessBuildPlayer attribute to implement this yourself. I made a tool for this purpose called XUPorter, which can make exporting and libraries setting easier from Unity3D to Xcode. You may want to see it on GitHub. There is a demo in the package and you may set your bundle under the 'folders' tag.