Box 14 is basically a memo field, information does not carry over to your tax return, you have to enter the housing allowance separately even if it is in box 14.
Turbotax appears to handle your situation correctly. For ministry #1, you will enter the W-2 and check the box marked "religious wages" on the page of uncommon situations. Answer that you were clergy, enter your housing allowance and qualifying expenses (up to but not more than the housing allowance), and check the box for "pay SE tax on wages plus housing allowance."
For ministry 2, ignore box 14. The question is, what is your actual housing allowance as designated in advance and in writing by your ministry. If your box 1 taxable wages are wrong, you need a corrected W-2, and should not file until you get it straightened out. If your box 1 taxable wages are correct, then enter the W-2, check the box for religious wages, and enter your correct housing allowance in the next box. On the next page, check the box for "Pay SE tax on housing allowance only."
Your second ministry is paying you incorrectly, as a minister (regardless of whether you have a housing allowance or not), you are exempt from social security and medicare tax and pay self-employment tax instead. The ministry should have time to get this fixed for 2021--they should refund you any SS and medicare taxes withheld so far in 2021 and they should correct their form 941 filings with the IRS. It's probably too much to expect them to correct the situation for 2020, and the choice in Turbotax for "pay SE tax on housing allowance only" was put in place for this kind of situation; even though it is technically incorrect, you already paid SS and medicare tax on the wages, so you only owe SE tax on the housing allowance, and this choice in Turbotax allows the program to handle that kind of situation.
If the wages you report on your tax return don't match your W-2, you WILL get an audit letter and a tax assessment. Your W-2 from ministry #2 should show that your box 1 taxable wages are whatever you agreed in your contract negotiations--presumably you agreed on a total compensation package which included a housing allowance, so box 1 should reflect the compensation minus the housing allowance. If the W-2 is wrong, the ministry needs to correct it. Correcting the box 1 wages in the W-2 is fairly simple. Correcting the social security and medicare withholding is much more complicated and requires amended at least 4 quarterly reports to the IRS plus refunding you the money, and as I said, Turbotax includes the "pay SE tax on housing alone" as a way to work around the ministry's mistake. But they should try and fix it for 2021 before they get in any deeper than the already are.
Make sure you and the ministry are aware that the housing allowance must be designated in advance and in writing by the appropriate authority (finance committee, board of deacons, or whatever). "In writing" can mean in a contract or a memo or the minutes of a meeting, but it must be in writing and the tax-free housing allowance can't be retroactive.
Also be aware that you are only entitled to a housing allowance if you are performing the duties of clergy. An ordained clergy person who is not performing religious duties is not eligible for the housing allowance and must be paid and taxed like any other secular or lay employee. For example, a pastor hired to manage the office or teach Sunday school and who plays no role in planning worship services or administering sacraments is not clergy for tax purposes, at least not in that position. If you are not actually in a religious role at ministry #2, they must withhold SS and medicare tax like a regular employee and they can't offer a tax-free housing allowance.
Generally read this, and see page 8 for the definition of clergy who are eligible for this tax treatment.
https://go.efca.org/resources/document/preparing-tax-returns-clergy
