When I talked about paclets, I was thinking about the built-in stuff. That is one of the major things I worry may break. I wasn't referring to user-made paclets. I still haven't figured out most of the paclet stuff (any help is most welcome with that effort ... all this being undocumented I can't—actually don't want to—write to support when I get stuck).

I see that you have quite a few directories that you would like to sync. Personally, the only critical thing for me is the Autoload directory, which I keep in a git repo. Of course, git won't synchronize automatically, but that may even be a good thing in some cases. To be honest, I did plan for synchronizing multiple machines at some point, but I haven't gotten around to doing it properly yet, so I can't comment on how effective this is.

I use Autoload instead of Kernel/init.m because it affects subkernels as well as the main kernel.

I would like to know how your experiment goes. Please keep us updated!

I just tried copying the Formats folder to Applications/importstuff/Formats (with a basically empty importstuff.m file to establish the context), that didn't work. You can however simply copy the actual code for RegisterImport and the import converter into a package in the app's directory and that will do the trick just fine. You obviously have to load the package before you can use Import with the new format, so that's a bit counterintuitive.

The FrontEnd folder inside a package works, and it makes sense for larger apps. But again, if you have something that's basically a stand-alone palette and wouldn't need a package for anything, things get counterintiutive.

Interesting point about the extensions in PacletInfo... Those are a little bit, erm, under-documented, so I'm not aware of a solution for formats. I'm still a bit torn about RegisterImport on the whole, but that's a different can of worms.