It is the first 90 day report of every 180 day stamp you get on DTV.
So when you stay the whole 180 days of the stamp and then leave you have to do your first report at day 90 or a few days after, then there will be no second 90 day report because you leave the country at day 180 or before.
When you re-enter it starts all over again wit first 90 day report in person.
Only when you do not leave the country after 180 days and get an in country extension, there will be a second and a third 90 day report, you can do online
If you want to use the visa legally, you need ongoing activity, some people think requirements stop after they got the visa, but that is stated nowhere, so there is no reason to believe that is true.
Chances getting stopped when you reenter the country are very low, but there is a risk.
What will happen in the future nobody knows, but if they want they can implement all kind of checks to see if you comply with the visa requirements.
When you apply for a visa, normally you only submit the page with personal data, not the stamps, so it will not make any difference to have a new passport when you apply for a visa.
At immigration they also have all history info, but I can imagine that a quick look at a passport full of Thai stamps can be an extra trigger to check, but that is only when entering the country.
It is not uncommon, more countries practice this and warn before that difference in fees will not be refunded.
A visa should match with what your reason is to visit a country, it is not a kind of entrance ticket you buy for a certain period, and then gives you to do what you want in a country.
That is your opinion, but it is also the responsibility of the applicant to choose the correct visa. When you select wrong visa, they can correct you, or reject the application. I think the correction is much more customer friendly.