Zybot, I do not think you are correct
If I go into through iCloud and look at those folders, they are all encrypted
I only see the file unencrypted when I go into through Cryptomator
Please explain how you think they can be read externally
Thanks
Mattis, I provided a document with instructions
Is there something specific in there that is not clear?
Thanks
On your second picture it is visible that you chose a folder within iCloud Drive as mount point. That means the unencrypted data will bi synced to iCloud Drive. You can also see the cloud symbol next to the folder.
Was not a criticism just a heads up notice. I tested your remarks and it worked for me. Thank you.
May I ask where you found the -oallow_root and -olocal flags. I would like to read the manual for the flags and what else is available.
I didn’t tested this yet, but as this is the solution to solve this problem, maybe the developers (@tobihagemann ) can build this in the app for the Mac, so everyone can use this automatically.
Under this scenario, unencrypted data is not synced to iCloud
Try it - if you go in to iCloud over the web or from another device you will not see data in that folder, even when it is mounted
Hey Yomama, I deeply appreciate your documentation, but unfortunately it has a very poor resolution. Could you share your instructions with a better resolution? (specifically the pictures of Cryptomator)
Thank you so much. 
However, it is a bit confusing when a hard drive is dormant in iCloud Drive. 
Well it was a bit of trial and error to get it to work!
I managed to have it working even without the addons -olocal -oallow_root for me it was enough to just move the mount point away from /Volumes/
Also -olocal is not recommended by the developer and marked as use on own risk and possible data loss
local
This option marks the volume being mounted as "local". By default, macFUSE volumes are marked as
"nonlocal", which technically isn't necessarily the same as a "server" or "network" volume, but is treated
as such by the Finder in some cases. For example, the Finder may not show "connected servers" on the
Desktop or in the sidebar in some cases. If you use this option, you can get around this "limitation".
However, wait! Don't be too tempted and think local is a magic pill that will solve all your problems. In
fact, it may mess things up more than you realize. The operating system can be more aggressive in
dealing with "local" volumes (a .Trashes. directory will be created, for one). You could run into mysterious
problems with Disk Arbitration and other system components. I don't know (and possibly can't know--Mac
OS X isn't all open source!) the side effects of using this option. Therefore, treat this as experimental and
use with caution. Moreover, please do not file bug reports that involve this option--reproduce your issue
without this option and then file a bug report.
modules
I guess I should’ve pointed out that I’ve written a bug report, where I suggested some workarounds:
So from what I read, those 2 commands allow spotlight to find files in encrypted folders, otherwise you cannot find them when doing a search. It had nothing to do with mounting.
So what exactly does each one of those do?