Apparently, in the past, there was the illegal formation system in this game. The penalties imposed were apparently a reduction in possession. Some of it still appear to be there.
The question is why should there be a penalty (whatever sort of penalty) just because you use of a formation that has at the back say only 2DC, followed by DMR and DML, or like you say a formation that has no ST. In fact, this make no sense, since playing with an extra midfielder instead of a ST might give you more ball possession, and also playing with DMR and DML might give you more ball possession. Penalties should be there only when the formation or orders you have selected are not appropriate for facing your next opponent. That is, reasons should be tactical or in terms of football, not just because a user did not make use of an ST or did not make use of at least 3 defenders..
Of course if a team plays a formation where all the players (except the GK) are on the side, then there should be a penalty, but in that case, the formation should classified as tactically inappropriate, and the penalty imposed should be in relation to what is tactically wrong in that formation.