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
* 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