It seems to me that you can save the comparison session to Beyond Compare (simply called sessions), which is the actual difference between the two filesystem objects. Those settings that you change above apply only to this session, but you want them to be applicable to any other similar session. I wonder if it might be a workaround to save a session with manually entered data comparison column parameters and change the file paths with the same formatting to force them to use the same column settings. Let me see ...
Let's consider three files
file1.csv
Column1,Column2,Column3 A,B,C A,B,C A,B,C1
file2.csv
Column1,Column3,Column2 A,C,B A,C,B A,C1,B
file3.csv
Column1,Column3,Column2 A,C0,B A,C,B A,C,B
The difference between files 1 and 2 is used here. 
And here I change the settings of the data comparison columns
Now there is no change between these two files with permutation columns. 
With this session saved, I then edit the address bar to replace the 2.csv file with a similarly formatted 3.csv file and wait to save if the column settings are supported, and it looks like this: 
So, I suppose, you could save these column parameters in an arbitrary session example, where later you will have to change the paths to the actual files that you want to split at this point in time. A little inconvenient, it would be much better if these settings were used as a pre-configured setting, just as in a folder comparison session you can save filter settings that will be applied to new sessions.
I'm curious why your dialogs are different from where I navigate to edit settings; in particular, you have a lunge that says "Use only for this view." What else is listed in this case? I am using version 3.3.8 (build 16340)