"When you say to withdraw the 2023 excess, how can I do that? The HSA custodian (Fidelity) seems to have only two relevant options for withdrawals:
1. Return of excess contribution form, which I cannot use because the contribution was from too long ago (2022). I confirmed it with them multiple times.
2. Normal distributions, which would generate the kind of 1099-SA that I received for my March 2023 withdrawal, with distribution code 1."
You did not understand what I wrote. I wrote, "3. Depending on your other entries, TurboTax might calculate excess contributions for you this year. If so, you won't be able to withdraw the excess from 2022 (the overfund amount that you entered), just the 2023 excess. Do so."
Let me say it again: If TurboTax tells you that you have an excess for 2023, you can withdraw any part of that excess that is not part of the carryover from 2022.
Steps 4-7 are how you deal with the $100 carryover from 2022 - as you note, it is NOT done by "withdrawing an excess contribution".
"The custodian is telling me that my tax advisor should be able to sort this out with the IRS and are not offering any alternatives." - this is no surprise. I have laid out a path for you to get your HSA back to normal. That is not the HSA custodian's job, and, frankly, the custodian generally knows less than they think they do.
"can I take that 1099-SA that I received and treat it as two separate 1099-SA forms?:
1. Return of excess contribution ($90: Not $100 because there is a $10 loss on the HSA from Jan 2022 to March 2023).
2. Normal distribution ($10) that I will apply against medical expenses."
Steps 6 and 7 describe how to handle this, without you changing the distribution code in the 1099-SA that you have already received (plus you splitting the 1099-SA into two). You express concern about the IRS not understanding what you did (which is good), but the way I outline involves less violence to the process.
In any case, "but there has to be a way to explain that to them", but there is no way in the current IRS instructions for you to explain this to them, so don't try. Just document everything we talked about here and what you did, in case anyone ever asks. Given the lack of IRS instructions for the HSA process and form 8889, it's all you can do.
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