Sql-server – Setting for default column type

No, there's no magic or hand-waving here. It'd be great if synonyms, say, applied to types, but that is not the case. If you want to make these columns first-class citizens, you'll need to change the table. You can automate this to some degree, though I won't post code to help with this unless you specify what you mean exactly by "manually" and why you think this will be a significant burden you want to avoid.

To automate this, you could say:

DECLARE @sql NVARCHAR(MAX) = N'';

SELECT @sql += CHAR(13) + CHAR(10) + N'ALTER TABLE '
  + QUOTENAME(OBJECT_SCHEMA_NAME([object_id]))
  + '.' + QUOTENAME(OBJECT_NAME([object_id])) 
  + ' ALTER COLUMN ' + QUOTENAME(name) + ' NVARCHAR(MAX)'
  + CASE is_nullable WHEN 0 THEN ' NOT NULL;' ELSE ';' END
FROM sys.columns
WHERE system_type_id = 99;

PRINT @sql;

-- EXEC sp_executesql @sql;

That said, you probably don't want to use these columns with distinct / group by anyway.

Taking @Mr.Brownstone's idea, you could definitely try this:

DECLARE @sql nvarchar(MAX) = N'';

SELECT @sql += N'
  ALTER SCHEMA dbo TRANSFER custom_schema.' + QUOTENAME(name) + ';'
  FROM sys.objects
  WHERE SCHEMA_NAME([schema_id]) = N'custom_schema';

EXEC sys.sp_executesql @sql;

Now, it may be the case that you have foreign keys etc. that will need to be dropped and re-created (and I've shown how to automate that too), or as I mentioned in a comment, you may have explicit references to custom_schema in your existing objects. You may also have duplicate objects (say, dbo.Customers and custom_schema.Customers) that you'll need to handle. But the general idea should be sound.

Another workaround would be to upgrade to SQL Server 2012, where you can set a DEFAULT_SCHEMA for a domain group. I haven't tested this, but this Connect item says it has been made so.

In either case, I still think the app should be fixed eventually. As I've mentioned many times before, you should ALWAYS use an explicit schema prefix when creating or referencing objects.