This refusal is self-explanatory . For a non-material amendment the LPA have to be convinced that the proposed amendment to the original planning application will not need to to be advertised, i.e. they will appear to be as originally approved. The list of amendments on this application will effectively change the look of the building from the outside, hence the application has been refused.
PAPA Says - Its a shame that the LPA did not take a look at this application at the point of submission, and make a call to the agent to confirm that a planning application would be required, although the decision was made only 3-weeks after submission, it might have saved the applicant a few further weeks delay.