Let's look at your questions individually.
1- For the remaining funds in my account, leave it there until 2025 and redefine it as a 2025 contribution. Refile 2023 claiming as income and pay subsequent penalties.
Yes to both. When you carry over an excess contribution, you are given a chance to use it as a valid contribution in a future year.
2- for the remaining funds in my wife’s account, fill out a return of excess form with the proper addendum (since what remains is lower than the excess funds, aka all of the contribution for 2024),which will bring the balance to zero. Include the 2023 contributions as income when refiling for 2023 and pay subsequent penalties. I was going to wait to talk to a tax expert about the addendum for return of excess contributions, but I see the wisdom of getting it done before end of 2024. Is the addendum likely specific to Fidelity (holder of our HSAs) or is that something a tax advisor could help with?
You should withdraw only those funds that have been identified by TurboTax as excess. When you amend your 2023 return, TurboTax will add the HSA contributions to your income tax, and you will pay income tax on that. There will be no "penalties".
As I think you know, excess contributions in 2023 cannot be withdrawn after 4/15/2024. Instead, they are rolled over to 2024 as HSA contributions, to see if you can use them in 2024. If not, then the aggregate of the excess will be rolled over to 2025, getting a 6% excess tax each year.
NOTE: on your 2024 return, you can withdraw only the excess from your 2024 return. TurboTax will not let you withdraw the 2023 excess (which is correct).
None of this is specific to Fidelity. Any tax advisor familiar with HSA processing can help you with this.
The "cheapest" way to deal with this is to try to apply any excess that is rolled over to the HSA contributions for a new year.
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