mask = pvt.columns.get_level_values('project_id') != 'All'
pvt.loc['subtotal'] = pvt.loc[:, (mask)].sum()
pvt = pvt.stack().swaplevel(0, 1).sort_index()
pvt = pvt[pvt.columns[1:].tolist() + pvt.columns[:1].tolist()]
Sub Total в сводной таблице pandas