Sorry for the inconvenience. The problem you detect is not related to lighting, but to a haze effect that is applied depending on whether an object is near or far from the camera, and gives the water its hazy appearance at a distance.

The problem is that this effect inside the water is applied in a later step to the drawing of the geometry of all objects and it is impossible to guess the distance of the objects that are behind others, even if they are transparent.

The shaders work by doing tricks to achieve the effects, and are limited by the infrastructure provided by Optifine/Iris, and Minecraft itself. Every shader highlights some aspects to the detriment of others, and it is a design decision.

In the particular case of MakeUp, decisions have been made to allow it to be fast without sacrificing much graphic quality, but it is impossible to cover all the flanks with this requirement.

The problem you point out is unsolvable in MakeUp's architecture. Sorry.