Except that if you challenge their claim, the burden of proof would switch. I'm a little out of my depth on the technicalities of the LN, but my understanding is that it would be ambiguous what the actual buy and sell prices are for the bitcoin that ultimately gets used to settle a transaction.

You might argue the capital gains were lower than the IRS is claiming, by identifying different monetary units as the ones that were used and the IRS would then have to demonstrate that your claim is false.

Even if I have some of the details wrong, that's the kind of messiness I'm talking about.