Confused about tense of Japanese


I read <https://japanese.stackexchange.com/a/25378/45347>, which says in
Japanese, main clause's tense is relative to now, and subordinate clause's
tense is relative to main clause's tense.

But I can't understand these two sentences, if the former means "I thought なおみ
was in the school", what does the later sentence mean?

> 私はなおみが学校にいると思った。  
>  私はなおみが学校にいたと思った。




I don't know how rigid tense concord really is, but according to (my
understanding of) the standard teaching English grammar in Japan,
私はなおみが学校にいたと思った should be translated as _I thought that Naomi **had been** at
school_. Since いた is inside the clause, its past tense refers to the past with
respect to 思った, which is already past, so that いた is actually pluperfect1.

On the other hand, いる in 私はなおみが学校にいると思った refers to the same tense as 思った, so
it is rendered as _was (at school)_.

* * *

1 I'm not sure it is the right terminology.

