Metashape will allow
but GeoTIFF format do not assume several resolutions in one file.
You can process it altogether and even export in best resolution (which will be equal to the resolution from the lower flight) but areas covered only with higher flight will contain interpolated data.
In other words, you will see what you want but GeoTIFF as a container will consist of lots of useless extra pixels. Not sure with KMZ.