How would his logical conclusions (ones in blue) not violate the all before some rule? Seems like that is exactly what it is doing...

The only is a group 1 indicator ... learned that from lessons later on. Tricky but apparently the way it is.

ditto

I believe you're on the right path. Essentially, since 5+ is the necessary part of the conditional argument, there is still a chance you can be 5+ minutes late but not marked late. If you recall, cat -> mammals (mammals are the necessary part) -- being a mammal is necessary to being a cat but being a cat does not necessarily mean being a mammal. Similarly, being 5+ minutes late is neccessary to being market late, but not all students who are 5+ minutes late are marked late.