I think you misunderstood Form 5329.
First of all, there are two different taxes involved here. When you take a distribution from an IRA you include the amount of the distribution in your income on your tax return, and you pay regular income tax on it, just like the tax on any other income. That's the first tax - regular income tax on the amount of the distribution.
What most people commonly call a "penalty" for the missed RMD is technically an "additional tax." The IRS forms and instructions consistently refer to it as "additional tax." The additional tax is calculated in Part IX of Form 5329. This is the second tax. It's in addition to the regular income tax.
I don't see any place where Form 5329 gives you instructions for adding a missed distribution to the tax return for the current year (2023). Line 55 of Form 5329 tells you to include the "additional tax," i.e. the "penalty," on Schedule 2 line 8. Is that what you're referring to? That's just the "additional tax," not the distribution amount.
If you requested a waiver of the entire penalty, line 54 of Form 5329 should have been zero and line 55 should have been blank or zero. Did your Form 5329 have a non-zero amount on line 55? Is that the tax that you are saying you paid, and that the IRS "accepted." That's not income tax on the late distribution that you took in 2024. It's the "additional tax" (penalty) for not taking the distribution in 2023.
The IRS may not know how much your RMD is, or how much you failed to take, except from what you report on Form 5329. If you filled out the form showing additional tax on line 55, they will accept that.
If you filled out Form 5329 incorrectly, you should include a corrected Form 5329 in your amended return for 2023.
I don't think Form 4852 is appropriate. The 2024 1099-R from Schwab is not incorrect. It is supposed to include all of the distributions that you took in 2024. You are supposed to include all of those distributions in the income on your 2024 tax return, and pay income tax on all of it.
