Those arguments sound a bit handwavy. If you have an application that runs into memory overflows without an explicit flush call in place, please submit a bug report about that. If that is the case, we definitely should not change anything in emscripten unless explicitly marked down to be a workaround for a bug, and link to a bug report, so that we don't sweep any bugs under the floor and forget about them. 

I wrote a demo to test this behavior. The test page https://dl.dropboxusercontent.com/u/40949268/emcc/10kCubes_flush/10kCubes.html?--objects&700 implements eglSwapBuffers with a call to Module.ctx.flush(). The page https://dl.dropboxusercontent.com/u/40949268/emcc/10kCubes_no_flush/10kCubes.html?--objects&700 is otherwise the same demo, except leaving out the flush.

In Firefox, I see the flush() taking 0.5-1.2ms on my macbook air laptop, so there definitely is a sync point there that impacts performance.

If there is some reason for having the flush there for observable correctness reasons, please submit a unit test about that to ensure correct behavior. Otherwise I don't see much reason to call glFlush here and we should leave it out.