I did this to combine U-Jagd Tools and Integrated Orders - the former mod comes with instructions for adding what needs to be added to the menu .ini file and a few changes that need to be made to existing entries. It was time-consuming but certainly doable.
I've also combined the commands_xx.cfg files of numerous mods with the ones from Integrated Orders, as have numerous other people, using the "contrast and compare" option that you describe.
I think with the example you gave, though, you may be looking at two different versions of one entry that is supposed to refer to one specific thing. Simply renumbering one version and adding it to the file may cause a problem when whatever it refers to has two separate sets of specifications controlling its size, location, etc.
Others will no doubt know for sure and be able to offer more advice.
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