Imagine yourself starting work in an office with 20 people, who had all been together for 5 years, how would you feel after just 10 weeks. You don't know the "in" jokes, don't remember all their names, don't remember where certain things are kept, have no back history, etc. So you learn coping techniques, and through experience you know it will get better. The people around our also know how rotten it is to feel like the new guy, so are warm, welcoming, and help you.
Your son's school is letting him down, by not giving him the right tool kit to cope with the feelings of insecurity, and not informing the other kids about how to involve newbies...it's not their fault, they have never been a newbie, they have no idea how horrible it is. As for teachers over looking him, that is just lazy, as they do not know his ability, character or name properly yet, do they opt for the ones they know about.
You need to very discreetly start communications with the head of sixth form, politely telling him, thst whatever processes are in place to integrate new kids, clearly is not working. He should be doing things like ensuring your son has projects to work on with small groups, that require time together outside school hours, making sure that pairings for science experiments are not predictable. Thry are still only young adults, and need a bit of social manipulation, they can be left to their own devices next year, when there are no new guys.
At the same time understand that the outsider emotions are all very new for your son, and very raw, but are all part of the horrible process of learning to be an adult. Some people can just throw themselves into the mosh pit, but it certainly is not the case for the southbucks tribe, parents included.