I checked and InkBox is indeed using filesystem encryption, as well as other measures that make it far more secure than the stock Kobo system.
https://inkbox.ddns.net/wiki/index.php?title=Main_Page
- Increases storage security by adding two-factor authentication (2FA). When the EncFS volume key is stored outside the encrypted source directory and into a physically separated location from the actual encrypted data, it significantly increases security by adding a two-factor authentication (2FA). For example, EncFS is able to store each unique volume key anywhere else than the actual encrypted data, such as on a USB flash drive, network mount, optical disc or cloud.[6] In addition to that a password could be required to decrypt this volume key.
Advantages
- EncFS offers several advantages over other disk encryption software simply because each file is stored individually as an encrypted file elsewhere in the host's directory tree.
https://en.m.wikipedia.org/wiki/EncFS
So that would appear to address two issues:
1. Your Ellipsa 2e is not supported by InkBox yet.
2. If you got it supported, you would still be missing the proprietary gesture recognition software. According to Quoth and others, this functionality is not as advanced in FOSS.
So you are relegated to keyboard input, or uneditable images of text, or maybe immature gesture recognition software.
Maybe you could encrypt directoryies instead of a filesystem, and only temporarily unencrypt the part that needs access or syncing? Not sure if it is feasible...
* Not implying this is a "secure" practice, as you are still open to corruption of the system, including by network attacks. Inkbox takes a total system approach which is more effective,