Welfare comparison - replicating Born and Pfeifer (2018)

I am not sure I fully understand the question.
Part 2 is straightforward: in your mod-file, you the baseline takes the place of the flex-price outcome. See also

Regarding Part 1: the macro language essentially allows you to combine several mod-files in one. You can use the savemacro= option to see the mod-file that results in this case. Because of this setup, you will always get the same structure of results, because you only change some equations and parameter-related statements in your file.