Security is compromise. You can share your whole home directory, if you trust the software, but it will make any kind of protection useless, or you can write a helper tool, which will grant access to a single selected file using a hard link, to make alias for file content, or synchronize files between directories, or mount a shared directory to both container and your home directory, or use SELinux to grant access to a selected directory only. Chose your own compromise.
But it doesn't have to be such a shitty compromise. Most desktop applications could be made such that you have all the security and the convenience.
Separate user for untrusted apps is the proven way to do that in UNIX. :-/
That can happen under the hood, but the user should not have to deal with that