I may be the person to whom you refer who suggested ignoring it. I am not a tax professional and I don't claim to have any special knowledge of what will or won't alarm the IRS.
My strategy is to try to do what makes sense, and not to assume that Charles Schwab and Company know what they are doing. This has worked well so far.
Amortized bond premium is something you can deduct from interest, so you can lower your taxable income and pay less tax. If you have it and don't report it, you may pay more tax than necessary, but you won't pay less. This seems unlikely to upset the IRS.
What alternative do you have?
You don't have a schedule A where you could deduct it as an adjustment.
You could just deduct it yourself and report less interest income (perhaps lie to TurboTax about what was on your 1099-INT), but that seems a lot more risky.
You could argue with Schwab or Intuit or both until you get them to agree on what makes sense to put on your 1099-OID. Ideally, you should study the tax publications and regulations to determine what should have been on there, so you only have to argue with the company that is wrong (probably Schwab). This would take a lot of time and a lot of puzzling over obscure documents and would probably fail in the end, so I wouldn't recommend it. (I have done this, although not with this exact issue. I have actually gotten Schwab to change their reporting, but it's much easier just to assume that Schwab sometimes does goofy reporting and report what makes sense, if you can even figure that out, than to try to reason with Schwab about it. Tax accounting for bonds is complex.)
Instead, I would recommend you generously donate to your fellow citizens the tax break you would have gotten by deducting the bond premium and just don't report it.
