is there any way to configure the line item discount to not round to 2 decimal places for every item and instead, round at the end of subtotal calculation?

I don't think so

any workarounds?

Maybe a script? Loop through the lines - do the math seperately (while acommodating for floating point issues) and then create a custom discount amount instead of a percent?

I think the rounding decision might also be to do with tax compliance. I had to do a script for this. The issue I had was to do with our 'estimated' tax calculation we did For partial shipment prepayments. Our prepayment estimates would be 0.01c different to what NetSuite ultimately invoiced. Then that 0.01 became an overpayment and appeared on statements until Accounts cleared out hundreds of the tiny amounts.