You can't negotiate fees with your bank. You can only negotiate repayment terms if you're struggling with credit card debt. You can always choose another bank if you don't like their terms.
Mid-market rate? Or say the Bangkok Bank TT buying rate, which would be the one that applies when you actually transfer money. Alternatively, the one that Wise uses for the amount you're trying to show (keep in mind that for large amounts, Wise won't quote if it's above 50,000 Baht as you can only transfer amounts above this to 3 banks, including Bangkok Bank).
Therefore, as a reliable exchange rate, I'd use the Bangkok Bank TT buying rate.
As long as you're flying into Vietnam and are thus able to switch passports, you can choose any of your passports to apply for the visa. Just make sure that it's the SAME passport used to enter Thailand. It doesn't matter if you used another passport to enter Thailand previously.