As you say, with colleges, all the students who are there have chosen to be there, and it is also easier for colleges to ask students who are violent, or really seriously disruptive to leave, than secondary schools. In terms of bullying, schools unfortunately do have limited options- it is very difficult to exclude before it gets physical.
Most school sixth forms are a nicer environment than KS3/KS4 as well. Part of that is choosing to be there, I'm sure, but I also think there's an element of maturity involved, Y12s in general are often much nicer to be around than Y9s.
Colleges and sixth forms also tend to have smaller class sizes, and the students get free periods within their day which allows them to decompress- they don't have to be on all the time.
I think KS3/4 would be much nicer for everyone in lots of ways if students were in classes of 20 max, I'm not saying it would necessarily make persistent absence less of an issue, but it might help some students. But there's no way that's going to happen without significant funding being pumped into schools.
More downtime in the school day might also help in some ways, but again you need space, you need staff to supervise it... it all costs money.
Many schools feel overcrowded, and I imagine they are hellish for anyone with sensory difficulties or who has anxiety- again, having more space costs money.
I also think the waiting times for ASD and ADHD diagnosis probably don't help- ASD is 2 years + around here.