I would have thought the acid conditions of the stomach would normally facilitate absorption rather than destroy the molecule.
It's possible very acid conditions or enzymes present in this environment could "breakdown" MDMA, but as a HCl salt, absorption in the stomach would normally be fairly quick.
As MDMA also stimulates 5HT3 receptors in the stomach, extra secretions could raise acidity slightly, but as to whether this would cause more destruction of the amine, this is hard to say. It is the liver which destroys much of the MDMA absorbed. This is why plugging is prefered by some people as it involves administration via a less acidic area which is further from the liver (reducing first pass breakdown)
If you take antacids too close to rolling, you may very well cause less absorption of MDMA in the stomach. The alkaline nature would react with MDMA HCl. Except for perhaps a little absorption in the small intestine, most of this freebase would pass through the gut.