I don't believe this is a bug.

By default user-setup/encrypt-home is setup using ecryptfs and uses the
user plaintext password as the seed for the ecryptfs key generation.
That way plaintext password is used in pam stack to authenticate user
against shadow password, and used to derive decryption key to decrypt
encryptfs. Clearly shadow salted password cannot be used to derive/setup
ecryptfs encryption key, thus the two options are mutually exclusive.

Using plaintext password is imho bad, thus instead do the install with
crypted password, and setup user-home encryption post-install using
"ecryptfs-migrate-home" command http://blog.dustinkirkland.com/2011/02
/long-overdue-introduction-ecryptfs.html

Given above deficiency what would you expect from the installer?
Critical prompt - encryptfs home was requested, but cannot be configured
due to missing plain text password?

You also report another bug too w.r.t make-user question. Not sure what
needs fixing there.

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https://bugs.launchpad.net/bugs/1578369

Title:
  preseed user-password-crypted password cannot be used with d-i user-
  setup/encrypt-home boolean true option

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