SQL Server: Enable Full-Text Search on model Database
Edited: It looks like the answer is:  No, you cannot create a full-text index in a system database.

You can, of course, run a script to turn on a full-text indexing after the new database is created from model, if that is necessary.  But by default all user databases in the more recent versions of SQL Server have full-text indexing turned on automatically.

Note that from SQL Server 2008 forward, the sp_fulltext_database command is a no-op, just supported for script compatibility.  

So, there is certainly no reason, unless your are supporting SQL Server 2005 or earlier version, to have this code included in your standard scripts.  It is obsolete.