You can use OOTB tables for this requirement as you are not changing the table definitions.
No SQL change is required.
You need to mention all the OOTB options when you say xml-combine as replace. Make sure that you are getting the correct repository xml file after combining by examining the template definition thro dyn admin.
One more good practice is use reasonably greater value to the code to your custom option (instead of giving the next number) as it would help during migration.
For Ex, in your example you have given code as 3 for your custom option. If ATG adds one more payment group they would use this code. If you use something like 100, it avoids the rework during migration.
Hope this helps.
Keep posting the updates / questions.