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.
saying nothing about retaining means it should be retained the whole period.
If it was allowed to let it drop, it would be described as with non-o retirement.
They will only check if they for some reason suspect you, or just coincidental because they might need to do a certain number of checks in a certain time.