The music option in NT is handled by some flevel script in each field screen that has random battles in it, and unfortunately flevel script is the most problematic part to share between mods (for instance, if you copied out NT's field script then you'd be getting everything else and not just the music option).
I think your best bet would be to add the command line that sets battle mode to not play the Battle BGM; it'd take an hour or two to get it done, but it'd be a case of just copy-pasting it into each field screen that has random battles on it. Open your flevel with Makou Reactor (make sure it has writing permissions and that you can save changes; do one field screen and try saving/loading it to make sure the changes persist) and then go into Field 116: md1stin; this is the first field in the game that you play on.
Click on the 'dir' group and the S0 - Init script. These Init scripts are the first thing that are run when a field screen is loaded, and are generally the best place to put a battle mode function. You want to add the command line to set the battle mode to not play Battle BGM right at the end, the line above Return (which is the end of the script) so click on Line 14 and then click on the green + button to add a line.
From the new window that appears, select Modules for the top drop-down menu, and then select Battle Mode 1 from the 2nd drop-down menu (the contents of the 2nd menu depend on what is selected for the 1st menu). You'll see a bunch of Flags all marked with a 0. Set a '1' in the third flag, and the text above should change to read: Battle mode: Do not play the battle victory music. This actually disables the Battle BGM as well so that field music plays instead.
Hit OK, and the new command line should appear in your Init script. Now right-click it and select 'copy', and get ready to paste that into the Init script of each field that has random battles in it (try to favour the Direct/Dir group when you can). The two problems that will arise with this are boss battles not using their specific BGM, and areas where the music is handled differently or that has no proper music (Great Glacier and certain fields in the Underwater Reactor for instance). To get around that, you'll need to either avoid placing the Battle Mode command in any field screen where a boss appears, or go a little deeper into the scripts and add a Battle Mode: None to the script prior to the command that starts the boss battle.
