Not too surprised they didn't fine you. Things were particularly confused regarding exactly how the amnesty for doing 90-Day Reports would end. It turned out that some offices required people who took advantage of the 90-Day Report part of the amnesty to file a 90-Day Report in August to get back with the program. Seems to me that your Immigration Officer took a very sensible approach to the matter in not fining you for what was a bit of a confusing situation. Now things are back to normal for you in terms of your 90-Day Reports.
The advice I gave to people staying a long time (advice I followed myself) was to simply ignore the 90-Day Report amnesty entirely. That is, continue to file when due because then you always know when you need to file the next one. The trouble with the amnesty is that people were told they didn't have to file 90-Day Reports without being told at the time how they would be expected to get back into compliance. I correctly guessed at the time that whatever pleasure was to be had in not doing a 90-Day Report would disappear in trying to figure out and complying with whatever scheme would eventually be announced to get people back to filing 90-Day Reports. I think I was right.
It's not that bad. Go to immigration and file a 90-Day Report in person (online likely won't work since you are overdue, but you could try that anyway). When you do that it will very likely be discovered that you were overdue on filing your previous 90-Day Report and you will be fined 2,000 baht. A remark will be stamped in your passport indicating the report was overdue. You will be given a new notification date to make your next 90-Day Report. There are no further consequences. It is in no way comparable to overstaying. It's a mistake that is easily corrected by paying the fine.
Suggestion for the future: put your next 90-Day Report notification date - 14 days in your electronic calendar. This will give you the first date you can file your online 90-Day Report. When your calendar alarm goes off, file the report online.
At Bangkok Bank, a teller can "force" an update to your passbook so if they do that and then produce your letter, account statement, and you make copies of the passbook, there will be an entry in each of those three things with a date and the same balance. Again, in my experience, those three things can be produced at nearly the same time. Phuket Immigration will accept a letter and accompanying documentation from the previous day when making an application. I understand that some offices require it to be produced on the same day you go to make your application.
It does make sense that if three proofs are required the easiest thing is for the officer to look for the same balance figure in all three places on the same date. It would also make sense to me that an immigration officer might understand when there is a discrepancy such as the one you mention. That's never needed to happen with my documentation in my experience though.
You don't say which Immigration Office you will be using. The answer to your question in Phuket is both:
"Signed and stamped bank letter AND Signed and stamped bank statement showing the money ( Minimum THB 400.000 ) for at least 2 months before application date. (Max 7 days old)
Copy updated Thai bank (saving account only) book name page and last 2 months transactions.
Please make sure that all papers have the same balance mentioned" --
The bank letter is a very standard format: full name of the owner of the account and balance on the letter date, signed and stamped by an authorized person at the bank.
The bank statement is simply a copy of the transactions that occurred in your bank account over a period of time that is stamped and signed by the bank.
A copy of your bank book shows the same information in your bank statement (assuming no consolidated entries in your bank book) but is not attested to by the bank (no stamp, no signature) and that you yourself sign as a true copy of your bank passbook.
The balance on the date of your bank letter should be the same in each of those three documents.
I recently switched to doing 30,000 baht withdrawals from Krungsri Bank ATM using my Schwab ATM card. Works fine. I used to use ACH transfer to Bangkok Bank's NY Branch but that went away due to a change in US government enforcement policies. I understand that Schwab Bank limits its maximum ATM withdrawal to $1,000. Have you been able to increase this limitation or to make counter withdrawals in Thailand using the Schwab ATM/Debit card greater than $1,000 (equivalent in Thai baht)? I have used TransferWise to bring over amounts in excess of $1,000, but the cost is greater than with using the Schwab card and ATM withdrawal.
Also, consider that you get the 200 baht fee for every ATM transaction so better to use Krungsri Bank (yellow bank) as it allows you to withdraw 30,000 baht max (machine limit) whereas, Bangkok Bank (blue bank) only allows you to withdraw 25,000 baht max (machine limit), and other banks I think have limits as low as 20,000 baht per withdrawal transaction.
On this date, MasterCard is better by 0.15 tbh per USD. Assuming your bank doesn't charge any extra fee, like for example foreign transaction fees. Also, note that some financial institutions like Charles Schwab will reimburse fully the 200 baht ATM fee charged by Thai banks.