I am in a similar situation, in that DS1 is awaiting a dx for Aspergers and DS2 is very bright, sociable and sporty. With regards to their achievements, I tend to focus on each one separately and make sure I praise them a roughly equal amount, even if their achievements aren't directly comparable, so for example DS2 comes home from school to say he has won the upper school chess tournament, he gets praise and a reward (we usually have a special dinner for big achievement days) then when Ds1 comes home and has remembered to go into the school office, deliver a message & come home with the reply, we make a song and dance about that as well as that is a big achievement for him.
The 2 occasions aren't comparable at all of course, but they both represent something that the child has tried hard and succeeded at which is the part that we focus on. I don't think it has done them any harm to know that there are different boundaries for each of them because they are each different. After all, Ds2 is very different to the kid next door who is the same age and also NT and Ds1 is very different to the Other kid in his year with AS. Their differences are as much because they are different people than being caused by their brain wiring and i believe that it is good for DS2 to learn to be more tolerant and accepting of those differences and for DS1 to become more confident with his own differences and learn how to look for the positives.
As for the independence thing, I'll get back to you in a couple of weeks and let you know if i am remotely qualified to talk on it. DS1 desperately wants to see Kung Fu panda 2 at the cinema. dS1 and i really don't and in a fit of stupidity, when DS1 was going on and on and on about it, I said he'd be going on his own then. Except of course all his peers go into town most weeks on their own or in groups, so now he wants to go. We have thoroughly talked through the route he needs to take, which buses he can get and their times, having his phone on at all times and that sort of thing. Tbh I think i will do something similar with DS2 when it comes time for him to go into town by himself although I probably won't go over it quite so many times or try to think up all possible variables and plan out a solution as he is more capable of thinking on the spot than his brother.
It is heartbreaking when they suddenly realise that their peers can do more than them. Today the door knocked and it was 3 lads come to call for DS1 to go out and play. When he got back he couldn't work out why I was so pleased and asked so many questions as people call for DS2 all the time. Except this is the first time anyone has called for him. In 4 years of living here.
But you know what? They are different and it is okay to treat them as such. If you push yourself to make things exactly even and identical between your SN and NT kids, you will end up doing both a disservice and running yourself ragged at the same time.