I think you can use it, so long as you avoid changing the following:
-) Character Lv/EXP (NT uses custom arcs, but Black Chocobo uses it's own built-in arcs which are set to default values. Even leveling up/down will auto-adjust EXP, etc.
-) You can add stats via 'sources used' but be wary of adding too many and then visiting the Rank-Up screen; in the current build, if you can't spend them all (as in, you end up with 255 in a stat) then you get stuck in an endless loop.
-) Equipment/Items can be adjusted with no problems.
-) Materia can be added/edited, just remember that NT uses adjusted AP. Mastered will always mean Mastered though so no problems should pop up there. Disabled Materia still have their original functions so Long Range, Stat Plus, etc. can be used. Worst that can happen with this is that you set a Materia to, say, Lv.2 and then in-game it's still Lv.1 or something but if you master it then it won't adjust down (Mastered is considered a maxed out value).
-) I don't think it has any variable editing outside of the experimental section, but be careful about using anything like that anyway.
Beyond that, should be fine. I think adding chocobo stables is actually quite touch and go, even if adding them to a vanilla game. There's a bunch of variables attached to them. Safest bet is to buy all the stables normally and then add the desired chocobo to them with the editor if you want to do that.
