One of the quirks of the current system is that subsidies are pitched as decreases to what one owes in taxes. There would be more transparency (but more overhead) if everyone paid full sticker price for taxes and then the govt separately gave money to the groups whose behaviors it wanted to encourage or whose challenges it wanted to help with (or fined the ones whose behaviors it wanted to discourage). This would not be feasible either politically. But it would bring transparency and clarity.

One way the government wins with the current method is when the non-refundable tax credit is greater than the amount you owe in taxes.