I am coming from Boxcryptor Classic, which is since some time no more useful due to replacement by subscription license. Not acceptable for me! With Boxcyptor it was possible to define a separate location for the key file. For me Cryptomator is not only a replacement, but much better!
With Cryptomator the keyfiles have to be located in the root encrypted vault directory. However I managed with Windows symbolic links to place the keyfile “masterkey.cryptomator” somewhere else. To be precise, this masterkey file is placed in my personal Veracrypt drive. A hardlink would be only possible, if the keyfiles are on the same physical harddisk, that is why symbolic links are the solution.
But you have to pay attention, the backup file “*.bkup” is created automatically from Cryptomator during mounting in the vault directory. The file name of this file seems to be constant, so a symbolic link is also possible. So I am synchronizing the vault to my cloud storage just without the two keyfiles. Access and syncronization from other PCs is possible with the same method (exclusion of keyfiles when uploading). A couple of good cloud synchronization tools allow such filtering.
Hard, junction and symbolic links are good to know and beneficial to use.
Best regards from Rudy
P.S.: On smartphones this method is probably not possible (I do not know and never tried hard, symbolic and junction links on Android). And please note, that symbolic links are NOT possible for the normal encrypted files in the Cryptomator directory. Seems to be a limitation/bug reported in [Github-Cryptomator](https://github.com/cryptomator/cryptomator/issues/879). I do not care for the masterkey files, because this is a totally different topic.