We already can set user's primary mail address (with option --mail-address) on user account creation. Please add an option to set user's secondary mail addresses by adding proxyAddresses attribute per secondary mail address.
A corresponding ldif record would like like:
It would probably make sense to just allow specifying the option for the e-mail address multiple times.
Shifting to tools, where the other half of samba-tool's bugs live.
Maybe someone will notice it there.