I got that setting idea from Kinggath, the mod author of Sim Settlements in his Builders Toolkit. The third line is a good idea to add anyway, because it enables you to have another copy of the Creation Kit open (for browsing vanilla files for example). Just know that the second line is the one you have to add for sure - it's mandatory. It doesn't hurt anything to have both lines in there in this case, especially since the valid line is below the invalid/less-valid line. well, when I finally got it working I had both lines in there, I got sick of messing with it, so I just decided to keep both lines. That's the magic line that everyone needs to have, and nothing can be below it that contradicts it or turns it off. But, the second line is the one you absolutely must have in there. But I chose to do a backup and delete the line from both files (your choice). Technically you should be able to delete the conflicting line from the CreationKitCustom.ini only and it should work (in fact that is the recommendation). I made a backup of both ini files and chose to delete the conflicting line from both of them. It was overriding my line and turning master loads back off again whenever the kit loaded. It was the same line I added but it was set to zero, and it was "under" my new line. The line was buried in the middle of the settings in the section, so I hadn't seen it. There was actually a conflicting line in my CreationKit.ini and CreationKitCustom.ini files.I eventually found the "right" line that needs to be added. A lot of the suggested lines I found online for enabling multiple master file loading were typed wrong, or they were slightly off, or they were just flat out incorrect.
Hey - I had the same issue but I DID solve it, and it does work now.