Ultimately, I think it's just not good enough. Even if you're updating iteration counts automatically (which is clearly not a safe assumption, and to be fair not something we did in EnvKey v1 either), and even with safeguards against weak passphrases, using human-generated passphrases as a single line of defense is just fundamentally weak.
That's why in EnvKey v2, we switched to using high entropy device-based keys for our root encryption keys. It's a similar model to SSH, except that on Mac and Windows the keys get stored in the OS keychain rather than in the file system. Also like SSH, a passphrase can optionally be added on top of the device key.
The downside (or upside, depending how you look at it) is that new devices must be specifically granted access. You can't just log in and decrypt on a new device with only your passphrase. But the security is much stronger, and you also avoid all this song and dance around key stretching iterations.