Per the category:needs hw testing tag, I tried this out (on a DS Lite). I can confirm the correct behavior is as shown in SuperrSonic's GIF of VBA-M. In mGBA, part of the mirror becomes translucent during the flashing screen effects, making the background's archway clearly visible where it should be blocked by the (opaque) mirror.
To supplement SuperrSonic's screenshot of the error in mGBA, here's a GIF of mGBA's behavior.
Can you confirm that the mirror and dark Meta Knight are brightened during the flash on hardware, and not just plainly visible during? Fixing that could be a major pain for me, and everything I know about the GBA's video hardware tells me they should be.