Actually Apple had to find solutions to some of the problems you mention when they transitioned to OS X:
* multiple resource forks can be presented as files in a directory, the directory having the name of the multi-stream file and the files in it named after the stream, e.g. "resources"
* for transfering data to other mediums/computers etc you can use container formats such as zip or tar, but with the unpacker having the ability to unpack them properly to a multi-stream file
* since on modern systems such as windows you can seamlessly file-browse into container formats such as zip so this is even less of a problem
* actually OS X to this day uses something like this for "Apps" as they are a special container/directory that you can browse into when you know the magic incantation
Not only apps, but many other types as well. And the organization technique is nothing magical, they’re just directories with an extension in the name, and usually some standardized structure. They’re officially referred to as “bundles.”
Apps are bundles, various plugins are bundles (audio units, pref panes for System Preferences), and if Finder didn’t treat them specially, you’d never think they were. In a shell, they’re just like any other directory.
* multiple resource forks can be presented as files in a directory, the directory having the name of the multi-stream file and the files in it named after the stream, e.g. "resources"
* for transfering data to other mediums/computers etc you can use container formats such as zip or tar, but with the unpacker having the ability to unpack them properly to a multi-stream file
* since on modern systems such as windows you can seamlessly file-browse into container formats such as zip so this is even less of a problem
* actually OS X to this day uses something like this for "Apps" as they are a special container/directory that you can browse into when you know the magic incantation