In September it's very unlikely to be shorts weather anyway, it's going to be trousers weather.
I would go with basics for winter, in the more traditional school colours and then let him choose if he wants to wear them in summer- gingham dresses came out here after the Easter holidays. The fabric of most school trousers is horrible, I agree- the M&S jersey trousers are the nicest we found.
In my DDs school, I don't think a little boy would get bullied in Foundation year for wearing those, but the chances obviously increase as the kids get older. Whether we like it or not, as they stand out from the norm, there is more chance.
Lots of boys here wear rainbow coloured coats though, which is a nice way to add colour and personality in the winter months.
I don't think they are anything like the stripe shorts you showed, and I also think it's perfectly clear that they are aimed at girls in the traditional gender stereotypes. I'm very much kids wear what they like, and my daughter has been dressed from whichever section has the brightest colours for the last 5 years- until school. She very much has an opinion now on whether something is for girls or boys, and would not happily wear a 'boys' item.