### 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)

uint16_t *bone16w = (uint16_t *)&uptr[base_offset + i * stride];
				bone16w[0] = bone_ptr[i * 4 + 0];
				bone16w[1] = bone_ptr[i * 4 + 1];
				bone16w[2] = bone_ptr[i * 4 + 2];
				bone16w[3] = bone_ptr[i * 4 + 3];
			}
			base_offset += 2;
		} else {
			glDisableVertexAttribArray(RS::ARRAY_BONES);
		}
		if ((uint32_t)p_weights.size() == vertex_count * 4) {
			glEnableVertexAttribArray(RS::ARRAY_WEIGHTS);
			glVertexAttribPointer(RS::ARRAY_WEIGHTS, 4, GL_FLOAT, GL_FALSE, stride * sizeof(float), CAST_INT_TO_UCHAR_PTR(base_offset * sizeof(float)));
			const float *weight_ptr = p_weights.ptr();
			for (uint32_t i = 0; i < vertex_count; i++) {
				uint16_t *weight16w = (uint16_t *)&uptr[base_offset + i * stride];
				weight16w[0] = CLAMP(weight_ptr[i * 4 + 0] * 65535, 0, 65535);
				weight16w[1] = CLAMP(weight_ptr[i * 4 + 1] * 65535, 0, 65535);
				weight16w[2] = CLAMP(weight_ptr[i * 4 + 2] * 65535, 0, 65535);
				weight16w[3] = CLAMP(weight_ptr[i * 4 + 3] * 65535, 0, 65535);
			}
			base_offset += 2;
		} else {
			glDisableVertexAttribArray(RS::ARRAY_WEIGHTS);
		}
		ERR_FAIL_COND_V(base_offset != stride, 0);
		GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_ARRAY_BUFFER, pb.vertex_buffer, vertex_count * stride * sizeof(float), polygon_buffer.ptr(), GL_STATIC_DRAW, "Polygon 2D vertex buffer");
	}
	if (p_indices.size()) {