The mod's installer is rudimentary, and just patches over the top of .lgp files rather than going into them and replacing specific files. The ones it patches are:
battle.lgp (monster models, battle backgrounds, and in-battle character models)
char.lgp (field models; this part isn't strictly needed as only a few models were changed)
flevel.lgp (field files & backgrounds)
scene.bin (enemy formations, stats, AI)
kernel (Spells, character stats, misc.)
Things like music, menus, minigames, and videos are left alone by the patcher but I'm surprised that backgrounds were still okay. Were they field backgrounds or battle backgrounds? As for patching back in the graphical mods, it's more than possible; the only thing the mod needs to do is add in the extra monsters for the game to read, the event script for the flevel, and the scene.bin + kernel.
But Bootleg is something I've not used, and I've no idea how it patches things. But from what I can see in the related thread though, it looks like the NT Mod is getting included with the next updated release of Bootleg (though I'd probably better get all the bugs fixed before then). I'm also working on putting a 7H IRO together which has the game only load in the extra stuff that the mod needs, leaving everything else alone (so custom character battle models, etc. could be used without incident). Problem with that is you'd also need the graphical mods to be in 7H IRO format and to run the game through the 7H Wrapper (which would take a little setting up).
But if you can add the graphical mods manually by decompiling the battle.lgp then it should work fine. One warning is to maybe stick with only replacing in-battle character models and battle backgrounds. I changed a few duplicate models that appeared in the battle.lgp with new monsters so be wary about putting in, say, an HD version of the Shinra trooper to replace all instances of a Shinra soldier.