GBARunner2 also recently added native screen-swapping, so there's no pressing need for it on the TwlBg side any more.
If I remember correctly, unless the image is intact in the top-left corner then there is one frame delay for the image to be displayed. I just vaguely remember this, so I might be completely wrong.
However, swapping the screens just changes the memory location at where the DS framebuffer is stored 3DS-side, so it has zero latency, because I'm just changing where the image is stored in VRAM. It's completely passive, one-time swap. And it can also be done at will without any side-effects (tried it, and it only causes epillepsy, it doesn't crash TwlBg).