There are fundamental differences. Loan waivers are for the people who have taken loans from Bank and could not pay off on time. So money would reach them.
In some cases 5 paisa less, because some back officers in remote areas would take their commissions from the affected parties. It will be difficult to control.
In the case of NREGS, officials and contractors collude and take away the major chink.
However, with the help of some NGO's, people have got their money from corrupt officials under NREGS in Andhra Pradesh.
So it just takes little awareness and some volunteers to change the situations.