I've run both my Stackers in "pseudo" BTX mode (ATX board reversed/flipped).
With the first case (right when they came out) it was a simple matter to just take the whole tray assembly and reverse it in the case (not reconfiguring the backplane assy. to real BTX).
My newer case required a tiny bit of trimming to do this...apparently CM has made some revisions.
Although I like the Stacker well enough to have purchased two of them, be aware that there are some issues you may have to deal with.
-It is easily the most hardware intensive case I've ever seen.
CoolerMaster will use five screws where anyone else would have used a clip...the rooftop plastic trim piece is held on with like six screws and it's just a decoration, not structural at all.
Fortunately you get enough hardware with the case to build a space shuttle, but watch out, CM mixes/matches metric/American threads in the case and it's easy to try the wrong one.
-CM uses threaded inserts swaged into the panels...a very nice touch (infinitely better than the typical "punch and thread" found in most cases), but they are sometimes not properly threaded- especially the ones on the mobo tray for standoffs.
If your standoff will not thread in easily by hand DON'T FORCE IT!
I speak from personal experience.
I had to rethread 4 of them on my last case (IIRC, they are 3x.5mm, but I could be wrong) and removing the broken thread from my initial boo-boo was a real pain.
Other than that, I love 'em.