I just realized I probably misunderstood what you're trying to do. If what you want is to set the video mode (screen resolution) rather than the game resolution on a per-game basis, then yes it does look like there's still no way to do that. The best thing to do for now seems to be to set a video mode that works well with the game resolution you want, and display the game's native resolution (via custom config) within that video mode. For example, I think a 320x224 game fits nicely on a 640 (or any multiple of 320)x240 screen.
You still need to figure out a way to get custom video modes over to your VGA monitor though. If HDMI is not working for you then a hat for VGA output like the Retrotink would be a good solution for you.