to be fair, i imagine the 100% employment thing is based around students graduating, it would be odd to boast about failing students who got the boot, besides, the school does have reason to remove students who are failing to achieve passing grades, considering the points process value in actual currency (yen), it is hardly a cheap program the school runs, it wouldn't surprise me they had these things in mind to simmer away the not too bright students and pave way for the 'future winners' of the school. Just my thoughts but i kind of imagine this system was something in mind from the start.
As for the teacher testing them, i kind of agree, the announcing his expulsion publicly didn't shock me much, she could be making an example of what is to come and simply using him as a point maker to others to scare them into taking school serious, it would be effective after all, and the threat was issued prior to the exams, I doubt they would cover it up with no explanation when they was already warned what was to come. I however agree the rest seems to be a bit... off, as you say she conveniently went to the roof, normally she would go to the staff room, but lets give her the benefit of a doubt, maybe she really needed a smoke, her handling of selling the point seems like it didn't shock her, i think she was to be fair taken back that they figured a way around saving him so effortlessly (i think she knew they would try and she probably was curious to see how). But i like your test theory, this did cross my mind as i read your post and then you put it there as i was thinking it, i doubt it was a way to scam money, it seems the money value in only really a gimmick for students to work harder to actually gain the nice life style and essentially punish them who don't earn such rewards, but class D seem to be an exception class in all years so testing them does seem something quite likely.
I do agree the school isn't likely based on academics alone, i don't mean such as abilities in say sports (sorry sudo) but as you say, the main guy & girl would both be class A or B at worse, after all, the main dude did slap a 100 without issue and seems pretty intelligent (at least with regards to his peers, and im speaking of the smarter ones here), the class D students who are smart are still class D but all lack or lets say have personality quirks, Main guy is unsociable and would rather stick to himself avoiding drawing much attention to himself, the main girl is smart and second to him but she has a unsociable personality making her unapproachable and rather... lets say 'harsh' way of putting things and Kushida clearly is obviously sporting two personalities, nice on the outside and dark on the inside. Seems a lot of D have issues, which would make sense to me why they are there. Though i can't deny my theory here isn't likely to be correct, i mean main girls brother clearly is nothing to brag about, smart, yes but he obviously has a violent side (and abusive) and is easy baited to anger - making him ideal for D but he is A if i remember correctly.