@zenon, please do not divert topics with unrelated issues. Your situation has nothing to do with rounding. You claim an actual error by the supplier, which is a completely different thing.
Well, it is a rounding issue, as you yourself note in “VAT was calculated on all six lines, whether they were adding to or subtracting from the total. All prices were tax-inclusive. But the merchant evidently selected the option of rounding all tax amounts to the next larger (more negative or more positive) cent on every line item when backing out the VAT amounts.” And it is also wrong on the part of the supplier, because Dutch tax rules stipulate rounding 0-4 down and 5-9 up, either on each item or on the total, but consistently using the same method. So both things are true, rounding error and fault of the supplier.
Your solution is the wrong approach because the Concept BTW Aangifte worksheet will not pick up your custom 21,1% tax code.
My solution is wrong because it is not a solution in the first place. It is one of the ugliest workarounds imaginable. As for conceptaangifte, it is only a help tool which I don’t even use. I want the ledger proper to have the right amounts, I take out a report with decimals, do the VAT declaration manually while rounding to my favour, and then use a journal entry to move the saved cents from tax due to financial profit. You see, legally speaking, you are allowed to round the VAT to your own favour, but then you still have to pay corporation and divident tax on the cents that you thus saved.
So, what should you do about this? Nothing. Get rid of your 21,1% tax code and apply the real 21% tax code. Enter the tax-inclusive prices for the payment so your bank records match the receipt. Ignore the one cent difference in tax for two reasons
Both reasons you give are valid per se, but I can’t do that, lest I want to be chasing ghosts at the end of the fiscal year. You see, human booking mistakes are inevitable, so if the books don’t close exactly to the cent, there is no way of knowing whether you have a single 10-cent discrepancy somewhere, or multiple serious errors (like inverting credit and debit) that just happened to almost cancel out each-other. In other words, pedantry is necessary not because the tax authority would penalise you about a cent (especially not the Dutch tax office, which is particularly relaxed about much bigger but honest errors), but because when things begin to slide you can no longer rely on your own figures.
With all that said, my original question was “is there a better way to solve this?”. I would appreciate any reply other than “don’t solve it”, including “no, there is not” and “yes, like this”.