This is a long thread with many comments. I don't know if this will be a meaningful contribution, but here goes:
1) Typical charge controllers have 4 wires attached. Two in from the panels and two out to connect to the "converter to battery bank" connection. The old controller will be wired correctly, so the gozinta and gozouta wires simply move from one charge controller to the other.
2) If you can't get an exact match for a recessed/flush mount,
consider adding a simple plastic wall mount panel to cover the hole, cut a new custom fit hole for the new controller, and you're back in business.
3) Virtually all factory solar-ready systems are wired with #10 AWG wire...rated at 30 amps. On your best day, if you're lucky, 400 watts of solar is likely to put out about 20+ amps. So, with 400 watts of solar, parallel is just fine. And the advantage of parallel is that each panel performs at its best despite shading and other issues that might degrade one panel's performance. Panels in series only perform in total as well as the poorest performing panel.
4) If you think you'll ever upgrade your solar to more watts, get an MPPT charge controller rated for more amps. Later you can decide if you want to wire in series parallel or upgrade your wiring so you can run more panels in parallel.
But the real challenge you mentioned can be resolved with a decorative plastic planel to scab over the open hole and cut to fit your new charge controller. It will look just fine and keep your MPPT controller right where it belongs.
That link to the wall repair panel is just an illustration after a very quick search. You can probably find something more elegant.