Is a penalty clause considered usury if the payment is dropped upon a single lump-sum payment? And is it permissible to choose the option that involves less usury between paying a penalty clause or dealing with a usurious bank when unable to pay in a single lump sum?

The penalty clause was instituted to compensate for actual damages; therefore, it must be commensurate with them. It is not permissible to be bound by it except under extraordinary circumstances beyond one's control. The stipulation of a pre-determined increase on the actual expense, regardless of the excuse or the actual damage, is incorrect. If you are compelled to choose between borrowing with usury or paying the penalty clause, then pay the penalty clause; because the prohibition of usury is absolute.