With the changes, the scores didn't change dramatically, and the asm.js version got a bit faster too, actually coming in closer to the native score than before, which is weird. Overall, scores got better across the board by about 8% or so.
The fact that asm.js does better now than it did before somehow suggests to me that there may be an issue in the NDK libc's malloc or free implementation, and that the better scores are simply allowing that issue to have more effect. This is another one of those programs which does a bunch of "biggish" allocs/frees repeatedly.
I'll put the updated charts up with an edit note shortly.