Folder "Plugins for Hybrid [archive]" contains original (non extracted) plugins. These archives are not used in installer. I just left them there as reference.
But inside "Plugins for Hybrid [archive]" there is a folder "Waifu2x-w2xc-r8-a9f064a" which is used by installer. That strange plugin use multiple paths. See INSTALL INSTRUCTIONS.txt there. I have no idea which parts of that plugin are used or not used, and why it was build like this. I just set same paths as described in INSTALL INSTRUCTIONS.txt. As i remember it was a discussion about this strange plugin installation on doom9 and l33tmeatwad explained that it just the way how it works.
So all those are parts of that Waifu2x-w2xc plugin. The funny thing is that Waifu2x-w2xc is rather legacy and very slow, but it don't need Vulkan SDK. l33tmeatwad recommend to use faster Waifu2x NCNN Vulkan instead.
Don't forget, that if you change app or folder sources (even if you rename new sources with same names), in Packages you need manually re-import them again to project. Packages use some sort of internal cache and without manual re-import of each new file or folder, it will put old versions into installer.
By the way it is easy to inspect and see internals of any already created pkg installer with Pacifist.app
https://www.charlessoft.com/
DMG made with DMG Canvas.app, but i guess there are a lot of alternative options for this. DMG can be done with Disc Utility, but in less pretty way.