Triggering form prefills when conditional logic is used?

Will provide code later today for this!

So I found and developed a fix for a bug, but it seems like the opposite of what you're describing. I think we need to examine this more.

I find that I can PreFill a field that is only visible based on matching Visibility Rules. In your example, if Fruit Type is 'Clementine', the Fruit Type dropdown will have the stored value 'Clementine' whenever it becomes visible, i.e. whenever Fruit is 'Orange' (whether Fruit is itself set via PreFill or manually).

The bug I see is that I can't un-PreFill, if you will, the Fruit Type even when the currently selected Fruit doesn't contain the stored Fruit Type as an option. So if 'Orange' and 'Clementine' and stored and I manually change the Fruit to Banana, the Fruit Type will be null (meaning there will be no value in the dropdown, as is the case whenever you try to set a value that's currently not valid).  Since in this case you'd want the dropdown to have the placeholder 'Select...' selected, you can fix it with this code, which changes the nulls to empty strings so 'Select...' is selected when necessary:

MktoForms2.whenRendered(function(form){
  var nullToBlankFields = ['Fruit_Type__c'];
  /* ---- NO NEED TO EDIT BELOW THIS LINE ---- */
  var currentVals = form.getValues();
      mktoFieldsObj = {};
  nullToBlankFields
  .filter(function(field){
    return currentVals[field] === null;
  })
  .forEach(function(field){
    mktoFieldsObj[field] = "";
  });
  form.setValues(mktoFieldsObj);
});