I'd argue that the game boy LCD's response time would actually help to sell the effect better. The flickering would look even bore like an in-between color thanks to that screen's ghosting.
In fact, here's an example of it being used in castlevania II. Real gameboy hardware.
When belmont goes ino the water, or in fact, when any item goes into the water, they start flickeing in a manner not too dissimilar to what I did.
The only difference being that i flicker alternating lines instead of the whole part of the sprite that is submerged.
Part of why I love the game boy is how the devs essentially "cheated" the limitations by essentially turning them against each other.
Intentionally using ghosting as a pseudo teansparency effect or for motion blur, or layering sprites to get more details, all those small tricks that make you wonder how they did it.
If you want, I can try to collect more footage of examples.