Well, it is a logical issue:
Generals on elephants command as regular and move as irregulars.
The -1 pip bonus from subgenerals and ally generals is received if:
General is regular and all elements in the group to be moved are regular.
First condition is satisfied (the general command as regular, so could have the bonus) but not the second (he moves as irregular and makes the group irregular. You pay +1 pip after the second move for example).