"It looks like they are spreading the income over 3 years but not the tax that was withheld."

Of course not. Tax withholdings are no different, whether from 1099 or W2, or even paid in Estimates. They are just amounts to be applied to what you owe for the year they were paid in for. Once you see if there is more paid in and a refund is due, you can decide not to get the refund, but to "let it ride" and apply to the next tax year.

You never pay in money and then expect to spread it over multiple years. For one thing, why would you leave it with the IRS? They should not have any of your money you didn't need to give them, any earlier than you need to give it, really.