We ditched file size obfuscation a while back as it was too big of an issue for non-local files (as required for the mobile apps). Whether you consider the file fragmentation a good feature depends vastly on your security targets. If you value privacy higher than availability and integrity, this certainly is a point for CryFS. With Cryptomator, we strive for the best of all three primary security targets, which does lead to compromises. But if you don’t have any issues during sync so far and prefer a CLI solution anyway, then I would recommend to stay with CryFS. This is, for the most part, personal taste.
That said, I personally dislike snakeoil statements on their website like “the security of CryFS has been proven”. While I don’t see a problem with the cryptography, I prefer to keep some distance from phrases used by all those “military grade security” bogus companies.