A_MSSQL_SKIP_ALTERNATE_KEYS determines whether alternate keys are used to form indexes during table creation. The default value of this variable is 0, which allows alternate keys. This configuration variable can also take values of 1 (on, true, yes).
If you set this variable to a nonzero value (such as 1), alternate keys are not used to form indexes, which speeds up processing if many writes or rewrites are being performed. (Note that a value of 1 may slow processing if the application is reading sequentially using an alternate key.)