You mean with the optional NT .exe? I'm not sure, I've never used Bootleg. To answer both questions, the mod itself can run with any custom models, so long as the extra models used by the NT Mod for new enemies are left intact (if these are deleted due to a graphic mod's installer then the mod will soft-lock when it tries to load an enemy model that's no longer there). So it depends on the graphical mod installer; my own installer is easy to use, but basic in that it overwrites the entire .lgp files rather than just adding/changing the files that are new. Anything that changes default-story bosses, field screens (but not field script/dialogue), the battle backgrounds, and/or the characters should be fine.
So the first step would probably be installing the NT Mod, and then applying graphical mods on top of it. If the installers for those graphical mods are more precise than mine, they should only alter specific files while leaving everything else alone. I've seen people playing the NT Mod with graphical mods on top so it's definitely possible. The models can also be added manually by decompiling the char.lgp or battle.lgp and then moving the HD models in that way, overwriting the old ones before recompiling it (ULGP seems to be the tool for that).
As far as the prototype .exe goes, it should run fine with whatever mods are installed but if you installed something like the Menu Overhaul or anything else that alters the ff7.exe then I'm not sure how that'll go. I think the best thing as far as that goes is to try it out. If it doesn't work, swap over to a normal ff7.exe and patch that with Menu Overhaul, etc. instead. The NT Mod was actually specced with a default .exe in mind; the new one is just an optional add-on and I'm not even sure if it's balanced (the materia bonuses/penalties are quite heavy and I predict it'll make the game a lot harder).
Edit: @Kalderasha, I just got the HextLaunch thing working. I'm compiling a .txt file with all the hacks I've found on the threads which can be enabled/disabled by adding or removing a '#'.