In my experience it's moderately unusual for maps to have large areas of white, but in this case you might be able to pre-process the original image file to change the white to a more identifiable colour.
Clear All Previously Loaded Maps check box could be made persistent; ........ In fact, it would better if there was just a one step Refresh and Clear button in the Map List dialogue box.
I thought it was. But I normally have it cleared as I certainly don't
want MM (potentially) deleting all the maps whilst I'm calibrating or working with them.
Another excellent feature would be an ability to create a Boundary Route (Box) automatically once you've selected your three/four calibration points, rather than having to draw a box and then select the option. It's an essential thing to do when calibrating maps, so it should be able to be automated upon completion of the calibration.
I can't see how that could work. The "boundary" may have no relationship to the calibration points (particularly if there are only three). Control over the correct boundary can be vital for creating the appropriate search or placenames files or for merging maps.