Let's start with the basics.

The vfs config file you are using tells the game the locations it should look for files in. Those usually are Data, Data-1.13, Data-mod, Profile folder, and the game looks from right to left, so if it finds the required file in Profile folder it will use that one, if not it will look in the Data-mod folder, then the Data-1.13, then Data.
Let's assume you have in your profile folder a JA2_Options.ini which contains only the data for the starting cash. If MERGE_INI_FILES is off, the game will find data for starting cash, but each and every other option it looks for will not be found in the ini file, thus it will produce the red warning about no value, and use the defaults. If on the other hand the MERGE_INI_FILES is set for JA2_Options.ini, the game will use the starting cash values defined in the profile folder ini and the values defined in the Data-mod ini for the others, or if it can't find them there either, in Data-1.13 or Data. If it fails to find them anywhere, then the red warning will appear again.

So, do you need to customize both files? No, you only need to customize the one in the profiles folder, and only the settings you want to modify. Those will override the ones in the other folders, but replacing the one in Data-1.13 with a newer ini file will prevent the red warnings from appearing, without invalidating your own changes.