Sent an email to LTR office, and they replied quickly. In conclusion, it seems there is no issue at all to do as I was thinking, rather it was just the lady in LTR counter who was not familiar with details.
Actually handy to have contact to ask questions like this directly in writing vs. the usual mumbling with vague and changing answers in Jomtien immigration...
-------------------
Referring to your inquiries, please see the answer as follows:
1. I visit in home country in July, and apply new passport while there (would be much easier and cheaper for me there than in Thailand via embassy in Bangkok)
Answer: Yes, it is okay to get a new passport form overseas.
2. I come back to Thailand in September, and show both the new passport and the old passport (with the LTR visa stamp) at immigration. I know that the validity of old passport would not be enough to enter, but I would have the new passport also.
Answer: Your current passport which contained LTR Visa is still valid. You have got a stay permit stamp equal to the expiration date of your passport which is 4 November 2025. Therefore, you can use it to enter Thailand in September.
3. I come to BOI office to transfer the visa in September after arrival to Thailand (old passport would have 1-2 months of validity left).
Answer: After arrived Thailand in September, you should transfer your LTR Visa to your new passport before your current passport expire on 4 November 2025.
Kind regards,
LTR Visa Member Team