I do not use the designer for making changes, so I have no particular experience with script problems. I did some years ago find that the designers were prone to errors, so I am not surprised that you have some problems. Nonetheless, you find the tools valuable.
From your description, you wind up with two scripts, but they are not identical. So the problem is how to treat the scripts. Or how to avoid any need to deal with the issue.
Database backups or database snapshots are a couple of tools that can help.
If you are using SQL Server Enterprise or Developer editions, you have the ability to create database snapshots. So this solution depends on your SQL Server edition and you rights on that server and how many people are sharing that database.
Scenario using a snapshot database and assuming that you have full rights to do whatever you want to with the design database.
First, create a SNAPSHOT database (examples from the SQL Server documenation):
CREATE DATABASE AdventureWorks_dbss1800 ON
( NAME = AdventureWorks_Data, FILENAME =
AS SNAPSHOT OF AdventureWorks;
Once you have the snapshot created, make your modifications in the designer and then save your scripts. If all is well, you get rid of the snapshot:
DROP DATABASE AdventureWorks_dbss1800;
However, if the designer glitched you would then use the snapshot to revert the database back to the point in time of the CREATE...SNAPSHOT.
-- Reverting AdventureWorks to AdventureWorks_dbss1800
RESTORE DATABASE AdventureWorks from
DATABASE_SNAPSHOT = 'AdventureWorks_dbss1800';
Because you reverted, you can repeat the designer steps with the database in exactly the same state as the first effort.
If you are not using a version that supports SNAPSHOT databases, you can do the same thing (perhaps more slowly) using BACKUP DATABASE and RESTORE DATABASE.