Issues with AppleScript scripting Mail
This is more of an extended comment rather than an answer, but comments can only contain inline code and not fenced code blocks.

I'm unable to offer insight regarding your first issue, as I am not using Apple Mail at present, but is probably a bug as I'm aware other users have reported that set the enabled of every account to false doesn't work, and that seems relevant to your situation.  The second issue is most likely a bug as well, but possibly one that can be worked around, given that the other enumeration constants you listed are still working.

To illustrate a test case, you can try and execute this line of code:

return "axmd" as constant


and you should get back the md5 constant used by Mail.  This doesn't need to be inside a tell app "Mail" block, but it can be and may make more sense to place it inside one in your final script when using the password enumeration code.  The enumeration code for password is "axct", and hopefully when you execute this line of (test) code:

return "axct" as constant


you'll get back the password constant.  Probably the best way to make use of this in your script is to do so something like this:

tell application id "com.apple.mail"
    set axct to "axct" as constant
                .
                .
    # Other bits of your code including where
    # you define "theAccount", which should be
    # variable containing a reference to an
    # object with class 'account'
                .
                .
    set the authentication of theAccount to axct
                .
                .
    # Rest of your Mail-specific code
end tell