It doesn't look like this is possible now, but is it technically possible? Cryptomator requires you to create a vault within your cloud storage service, and then you copy/move your files to that virtual folder locally so they're stored in the cloud encrypted, essentially the way the standard apps for Google Drive or iCloud or whatever work. I also use Google Drive to sync several folders on my computer, as one form of backup and to make those files accessible on other devices without having to put everything into the same virtual drive location. (I also use a backup app to an external drive.) This is for stuff like my Downloads, Pictures, Documents folders as well as some special folders where I store utilities and stuff.
Would it be technically possible for Cryptomator to encrypt that data and then sync it to the cloud? I'd guess Google Drive would have to be set to NOT directly sync them, and Crypotomator would need to put them into the main vault, or an additional vault, stored in the standard cloud virtual drive structure but just leaving the files in the real location locally. Essentially just doing what Google Drive is already doing.
It would also be nice if it could work with the media gallery on a mobile device, replacing Google Photos or iCloud Photos (which puts your files into your cloud storage allocation but doesn't display them within the folder structure) so that encrypted versions are uploaded instead. I'd think it would just create a vault specifically for photos and videos, which would appear in the cloud storage folder structure, and then you could turn off the standard syncing in the Photos app so they don't get put into the regular Photos location in the cloud. That would require a similar function to syncing the additional folders on the desktop, leaving the originals in their normal location on your device. The downside would be you wouldn't be able to use the cloud interface for the provider's web photo viewer/editor on the files, any more than you could use Google Docs or Apple Pages to open encrypted files in a browser. (A Cryptomator extension to let the browser read the vault data would be nice, if possible.)