### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

case GLES3::CanvasShaderData::BLEND_MODE_LCD: {
					glBlendEquation(GL_FUNC_ADD);
					if (state.transparent_render_target) {
						glBlendFuncSeparate(GL_CONSTANT_COLOR, GL_ONE_MINUS_SRC_COLOR, GL_ONE, GL_ONE_MINUS_SRC_ALPHA);
					} else {
						glBlendFuncSeparate(GL_CONSTANT_COLOR, GL_ONE_MINUS_SRC_COLOR, GL_ZERO, GL_ONE);
					}
					glBlendColor(blend_color.r, blend_color.g, blend_color.b, blend_color.a);
				} break;
				case GLES3::CanvasShaderData::BLEND_MODE_MIX: {
					glBlendEquation(GL_FUNC_ADD);
					if (state.transparent_render_target) {
						glBlendFuncSeparate(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA, GL_ONE, GL_ONE_MINUS_SRC_ALPHA);
					} else {
						glBlendFuncSeparate(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA, GL_ZERO, GL_ONE);
					}
				} break;
				case GLES3::CanvasShaderData::BLEND_MODE_ADD: {
					glBlendEquation(GL_FUNC_ADD);
					if (state.transparent_render_target) {
						glBlendFuncSeparate(GL_SRC_ALPHA, GL_ONE, GL_SRC_ALPHA, GL_ONE);
					} else {
						glBlendFuncSeparate(GL_SRC_ALPHA, GL_ONE, GL_ZERO, GL_ONE);
					}
				} break;
				case GLES3::CanvasShaderData::BLEND_MODE_SUB: {
					glBlendEquation(GL_FUNC_REVERSE_SUBTRACT);
					if (state.transparent_render_target) {
						glBlendFuncSeparate(GL_SRC_ALPHA, GL_ONE, GL_SRC_ALPHA, GL_ONE);
					} else {