Tod Daniels I promised you an update as I sparked some confusion if it's possible to do 90-days notification online with passport acquired in the consulate in Thailand and without leaving the country (TM.6 card with old passport number). I did it once before and successfully did it again yesterday (application sent online yesterday evening and confirmation received right now, next day in the morning).
The timeline:
Jan 2020 - I flew to Thailand and didn't leave since then
Jun 2020 - Got new passport in consulate, stamp transfer (Immigration Division 1), 90-days notification in person
Sep 2020 - 90-days notification in person (I just forgot to do online when it was a right time)
Dec 2020 - 90-days notification online
Mar 2021 - 90-days notification by registered mail (website under maintenance)
Jun 2021 - 90-days notification online
TLDR : Answer Summary
The user successfully completed a 90-day notification online using a new passport acquired from a consulate in Thailand, confirming that it is possible to do so without leaving the country. The user had transitioned through various notification methods, including in-person and by mail, before finding success online.