We just implemented the possibility to store changes on files opened with Cryptomator directly back to the cloud. This feature will be available in the next beta release 1.4.0-beta2 
.
Currently, there is just one (big) problem left with Microsoft apps: as described in this post, we’re storing the decrypted file in the internal storage of Cryptomator on which only this app has access. If opening the file using any Microsoft application (e.g. MS Word or Excel) the shared file (with read and write permission) is still read only. This is because a problem in their application and hopefully will be fixed soon 
. Unfortunately, there is no workaround.
If you’re interested, here are some sites, which describes the problem: Link1 Link2 Link3 Link4