If you stay more than 90 days continously in the country, you need to file the 90 day report, called TM-something. I've heard the first one must be done in person, and the subsequent ones can be done online. If you never stay more than 90 days at a time, then you don't do anything. (I've never stayed more than 90 days in a row in Thailand yet).
sometimes there isn't an "only" country, but more than one country. You can have several passports and/or residence cards. I'm entitled to live either at my country passport (Costa Rica) or my residence country (South Korea, I have a residence card, equivalent to the US green card, where I've been living continously for the past 15 years straight).
so what about the PR holders you mention, they're also foreigners, aren't they? So in theory, they would also need to file the form, and be able to choose Thailand.
since my first visit to Thailand (August 2024). Some days they instruct people to use the e-gates, some days don't. But I think the plan is to use the e-gates only in the near future. That's why in my passport I have some exit stamps (but more entry stamps).
Sometimes they ask for something you've already given to them. Then, just give it again. I have an application ongoing for my mom. They asked as additional documents something that was already given, the only thing they added was "all in one single PDF*". I just did like they asked, now waiting.
* they're not on the same subject, so on the original form each PDF was uploaded on its respective category.