Solved it, used useState instead of useRef, and it solved it.

const [map, setMap] = useState(null);

useEffect(() => {
    if (dss_rowData && map) {
      map?.setCenter({
        lat: Number(laty),
        lng: Number(longx),
      });
    }
  }, [rowData, map]);

ref={(ref) => setMap(ref)}

I never did figure out why the re-render wasn't being triggered properly by the useEffect() call as we would expect it to. However, I figured out a workaround for those interested.

in the MapboxMap component, I added this:

  const mapRef = useRef(null);
  useEffect(() => {
    if (mapRef?.current) {
      mapRef.current.zoomTo(mapRef.current.getZoom());
    }
  }, [props.displayUploadedFiles]);

It goes into the underlying mapbox-gl map object and, whenever more files are updated, it "zooms in" to the current zoom level. This has the effect of if I were to pan the map manually, but automates it. It forces the map to re-render and makes it so the user can't perceive the viewport change.

changed from useRef() to useState and it worked, useState triggers re-render which worked perfectly.

const [mapRef, setMapRef] = useState(null)

 useEffect(() => {
    if (mapRef) {
    mapRef?.setCenter({
      lat: rowData?.laty,
      lng: rowData?.longx
    });
   }
  }, [rowData,mapRef]);

<Map  ref={(ref) => setMapRef(ref)}/>

I struggled with this recently. This is what I have done:

From outside, I made the ref for the map

  const mapRef = createRef<MapRef>();

  const mapContextValue: MapContextProps = {
    map: mapRef,
    container: null,
    isDragging: false,
    eventManager: undefined,
  };

  return (
    <MapContext.Provider value={mapContextValue}>
      ...
      <MapViewComponent />
      ...
    <MapContext.Provider>
   ...

Then in MapViewComponent I use forwardRef to put it into the ReactMapGL

<ReactMapGL ref={forwardedRef} ...>
   ...
</ReactMapGL>

So far the typescript stops complaining, but I DON'T KNOW is that correct way or not. I can't believe I can't find an example about this on github and/or google.

Really appreciate if we can get more insightful comments from people have more experience on this.