Those are the issues where I have accepted my faith currently and decided to not waste too much time but life with sub-optimal compromises.
I personally find their communication concerning end-to-end encryption on their website very misleading. It has been in Alpha for a very long time now.
Looking forward to an initial release that has worked out some of the current main issues:
Missing EXT4 filesystem support
Does not support EXT4 filesystem – unless rooted. Did root my phone but switched back as I am a big fan of OTA updates directly from Google.
No native Encfs support
Supports Encfs only through third party apps.
No Encfs support
Does not support Encryption (Encfs): see open issue in Chrome OS bug tracker
Workaround is to go through installing a supported GNU/Linux distribution via Crouton (quite the overkill solution) or use beta Linux integration (much less overhead but does not integrate into Chrome OS filesystem/file manager… also copying between the two systems was very slow on my system).