You say primary schools are different, but in primary schools firstly of course the children are younger and most want the approval of the adults in their life and haven’t yet developed stroppy teenage attitudes. It’s like saying "my eight-year-old does what I tell him so why won’t my fifteen-year-old?"
Secondly, in primary schools children are usually taught by just one or two main teachers over the course of a week, and develop a relationship with them. In secondary schools it is very different, with pupils often having a different specialist teacher for each of, say, ten subjects. The teachers may teach a couple of hundred children each week and can’t develop proper relationships with them all.
As for your opinion that it is not rude, disrespectful or disruptive for pupils to turn up late to a class, I really don’t understand that. Even if the pupil enters and takes their seat quietly (unlikely), if they have missed the first say ten minutes of the lesson where the teacher has given input and explained what he/she wants the pupils to do, what do you expect will happen? The options are that the teacher has to go through it all again just for them, or another pupil is asked to explain and has to waste their own time doing so, or the latecomer does nothing of any value. This last option means that at some point later the teacher will have to take the time to explain to them the input they missed. Why should they have to take time away from others who turned up on time?
Unpunctuality is discourteous to everyone else, at all ages. I don’t understand why you think it is acceptable. Pupils turning up to a lesson without the right equipment or books cause disruption and delay for everyone while the problem is sorted out.
A school is a microcosm of society. Society functions by the majority following the rules that society has decided are worth enforcing. Punishment for law-breaking contains an element of deterrence, to deter others from doing the same thing. I agree that some schools have rules I don’t think are worth having, e.g. specifying the exact type of shoes that may be worn, but if you don’t like the rules a school has, send your child to a different school.
All this, of course, assumes that pupils have the capacity to follow the rules. If they don’t, they may need help. Unless they have Special Needs recognised by the school, the people in the best position to either help the child themselves or talk to the school to point out the child's problems, are the parents. @Unexpecteddrivinginstructor has given you some very good practical advice.
If you encourage your child to think that they needn’t follow the rules that others follow, or even make any attempt to do so, and should not be penalised in any way for such actions, I’m afraid your child is going to have a difficult life.