Hello and welcome to the forum.
There is more information in the 'Parenting Children with HMS' section but I moved your post here into the intro so we could all welcome you!
I have been where you are for myself and with my kids, I also tend to over-worry about everything including schooling and bullying mainly as two of mine were bullied at primary at it was anightmare. But it is always stressful when our children move through the school years and to me personally the secondary transition was 10x worse than the primary one!
I want to say something to make you feel more confident but personal experience suggests that we dont tend to believe that it will be ok and that school will look after our kids, keep them safe and help them to develop self-confidence and self esteem.
A lot of children when they hit puberty put on weight and I can promise that he wont be the only child there who is overweight and it will change naturally but there are a few things you can do to help it on the way.
You say he has done the MEND programme so he must have the basics to hand. My children dont currently have a weight programme but that is purely because they are so active, but my middle son did get some puppy fat last year (13yrs), this did come off completely within 6 months. But I think that may have been helped by our family diet changing as I needed to desperately lose some weight. We follow a healthy eating plan at home and the kids have lots of fruit to hand and no crisps/chocs or sweets in the house. They do spend pocket money on the sweets though...even I havent managed to stop that!
There are lots of exercises that kids with HMS can do, it can feel that they are limited in their choice but in reality they arent. We usually dont advise contact or high impact sports but swimming/cycling/walking/ gym and dance and even things like wii fit can make a huge difference...on top of his usual exercise programme from physio. Encouraging children to play out with friends also makes a difference. Walking instead of taaking the bus also helps.
the one thing I have learnt over the last couple of years for my own HMS and my childrens is that everything has to be done in small steps, and you can both do this together and encourage your whole family to take part. But to be successful you have no choice but to take it slowly and do it in small steps. Without forgetting the need to pace as well if necessary.
Somehow you need to get the message across gently to your son that exercise (activity may be a better word! exercise may sound off putting!) is a priority and a daily thing which has to be done so he can lead a healthy life, with significantly reduced pain and fatigue. At the end of the day diet, activity and following exercises prescribed is all going to make him stronger and more able to cope with all of it.
Can he build up to walking to school? or is it genuinely too far for him to do so? Is it planned to have him take part in PE?
Have a family meeting and plan to change eating habits, and to start new activties together. In theory he could healthily lose several pounds before he starts secondary school. There is a certain slimming plan which if the parent is a member will allow pubescent children to join in free of charge with special ifnormation booklets but that is up to you and I cant name it for advertisement reasons. Dont get too worked up about the need to 'diet', you really dont at all you just need to eat healthily and increase activity.
I started a healthy eating plan 6 months ago with my mum after doing a further 6-9 months of my own physical rehab. I didnt believe we could lose the weight because I have mobility restrictions and take so much medication etc and yet I have lost 2st 5llbs as of last week and my mum with exactly the same limitations has lost 4st! I go to the gym 3x a week to use the toning tables and to swim, i cant do weights or gym equipment because it causes me injury but swimming and the toning tables has helped enoromously. Admittedly I did pilates, physio and hydrotherapy for months before I even started but it can be done....just slowly thats all.
As I said at the beginning I was a nervous wreck this time last year about my daughter starting secondary school because she has so many difficulties relating to her EDS and other things but I neednt had worried. She has completely blossomed over the year she has self-confidence and a higher self-esteem...the problem I have now is that she will not stop playing out and going to school so she gets completely exhausted and school attendance dropped a tad, so we changed a few things so she was more able to cope with school. Now we argue when I put my foot down and tell her she cant do things or she has to come in because she will exhuast herself...last week she tried skateboarding (

) and ended up breaking her arm and now is in plaster from above the elbow at 90degrees for teh summer hols! So she is restricted in what she can do now! hee hee! Mind you that hasnt stopped her I am still having to drag her in...she has done the GOSH programme, Pain management and is under physio and OT still now, she has a lot of medical appts but with her increased stamina and overall strength, some pacing (!) and healthy eating she is doing fine.
Speak to school if you are worried about your son. Explain what concerns you have, quite often schools are great about these things as know school wants to have a brand new school pupil bullied and they can help keep an eye on him. There may even be social clubs which other kids with low self esteem and confidence will be encourgaed to attend so that all develop friendships and dont feel isolated. Keep the communication lines open with your son but dont let him know you are worried, otherwise he will feel that he really does have something to worry about and that he wont cope...so start of with small steps and take some deep breaths!
we do have a school booklet in the shop that you can buy or download for a reduced price. It doesnt cover much about bullying etc but it can help school to understand the issues with HMS and may be he will be entitled to some extra support. Your son is about to enter the most exciting period of his life, the friends he will make now will stay with him forever and by Xmas you could be wondering what on earth you were worried about!
I hope this has helped as I tend to waffle and write an essay!