Stretch = blur, blur = ugly. Especially on a low resolution system like the SNES, even more so when there will be only a small amount of stretch. It also seems that I misunderstood your original statement, I assumed that you meant the stretching would be required for the 3D effect to work, not that it could be used to hide some of the edges.
As for what SparroHawc said about it being too much work, I can't see how. SNES9x already allows the user to enable/disable each bg layer, which proves a couple of things, 1. the layers are already rendered separately and 2. the emulator already knows the priority of each layer, or else it wouldn't be displayed correctly to start with.
Really all that needs to be done, even i it is on a per game basis, would be to render one display as-is, then a second with the layers shifted to the side (by different amounts of course). All of which can be don automatically as the emulator already knows which layer is in front, which is second etc. "It's a minor gain for a lot of work" is just a way of saying "I don't want to", which is fair enough.