Thank you your post into the forum.
Unfortunately you have to load your scripts into SSMS and modify them to update with your fixed value.
SQL Data Compare was designed for the user to compare two data sources and generate a synchonization script so that both data sources become identical.
You could possiblily achieve what you are seeking using our SQL Data Generator product, where post synchronization using SQL Data Compare, you use SQL data Generator to update the required columns with your fixed value.
Further information regarding SQL Data Generator can be found here.