Before they are dressed the Matrix stones are flat within .001", probably less, because there is no stress when making them so they don't distort and the mold cavity bottom is a flat plane within .0002" or less. The thickness of the resin stone and back will vary some with the coarsest stones being the worst and the finest stones the best, the big diamonds get in the way of locating the backs. Check the resin side of one Matrix stone against the back of the other, the machined blanks are also dead flat so they are an excellent reference surface. The gap in the photo can't be from the Matrix stone, that looks like about .02" which is huge! If the lapping plate is old and hollowed out in the middle the ends of the stones will be thinner but only a few thousandths of an inch if no one is paying attention. The coarser the stone the longer it takes to dress off thickness, it takes about 2 or 3 minutes to remove .001" from one end of a Matrix 250 stone if you really try hard with lots of loose grit.
I have a few questions:
1) What Matrix stones do you have? 250 and 650?
4) Are you using a guided sharpener or freehand? If guided which one?