### 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)

PolygonBuffers pb;
	glGenBuffers(1, &pb.vertex_buffer);
	glGenVertexArrays(1, &pb.vertex_array);
	glBindVertexArray(pb.vertex_array);
	pb.count = vertex_count;
	pb.index_buffer = 0;
	uint32_t buffer_size = stride * p_points.size();
	Vector<uint8_t> polygon_buffer;
	polygon_buffer.resize(buffer_size * sizeof(float));
	{
		glBindBuffer(GL_ARRAY_BUFFER, pb.vertex_buffer);
		uint8_t *r = polygon_buffer.ptrw();
		float *fptr = reinterpret_cast<float *>(r);
		uint32_t *uptr = (uint32_t *)r;
		uint32_t base_offset = 0;
		{
			
			glEnableVertexAttribArray(RS::ARRAY_VERTEX);
			glVertexAttribPointer(RS::ARRAY_VERTEX, 2, GL_FLOAT, GL_FALSE, stride * sizeof(float), nullptr);
			const Vector2 *points_ptr = p_points.ptr();
			for (uint32_t i = 0; i < vertex_count; i++) {
				fptr[base_offset + i * stride + 0] = points_ptr[i].x;
				fptr[base_offset + i * stride + 1] = points_ptr[i].y;
			}
			base_offset += 2;
		}
		
		if ((uint32_t)p_colors.size() == vertex_count) {
			glEnableVertexAttribArray(RS::ARRAY_COLOR);
			glVertexAttribPointer(RS::ARRAY_COLOR, 4, GL_FLOAT, GL_FALSE, stride * sizeof(float), CAST_INT_TO_UCHAR_PTR(base_offset * sizeof(float)));