Then don't use that /exact/ setting - take the pieces you need? The academy, the frequently-absent headmaster, things not always being /exactly/ what they appear, in the OMG!Narnia* sense? Set it anywhere, anywhen you want - or don't /set/ it anywhere - have it be fluid.
I'm not familiar with Dr. Faust's academy either, but I like the basic idea of a place that is tied to all worlds, and possibly having students that are not, entirely, all what they appear to be. I like it a lot better than the idea of a 'typical' modern school setting, which I am not really all that comfortable with myself.
*insert alternate world, era or other such reality-bending insanity, depending on what's wanted by the player.