In my experience, isolation is used to prevent exclusion, and of course so the rest of the students can actually learn in a decent environment. You can't include a seriously disruptive student in a class at the expense of everyone else, and the pastoral system will support the individual causing the difficulties in the appropriate way.
In the schools where I've taught, the teacher sends work to the isolation room for the student to do. The room has partitioned booths, and is supervised by a teacher. It's meant to be boring as a deterrent, but work is always provided so it's not a barrier to learning. The students are always encouraged to 'earn their way back' into the classroom.
In a world where schools are condemned for exclusions and alternative provision services are woefully under-funded, isolation works well as an option within a limited range of sanctions available to a school.
As for SEN students, having worked for years in a behaviour unit, I would say that the crossover between SEN and behaviour in some kids means it's often impossible to split the two (of course many SEN kids don't have these issues!). Its important to note that SEN can mean a range of things. If someone has dyslexia but punches someone in their class, they are an SEN student but still have to be sanctioned like everyone else IYSWIM? The only exception I can think of in this situation would be ASD type conditions, where acting-out behaviours can be triggered and need to be handled more sensitively. Although if there are violent incidents, of course they need to be sanctioned appropriately too. Most schools have an SEN unit where students can take themselves if they feel overwhelmed etc.
When isolation units are well managed within a system of sanctions, they are an effective tool. Do all schools use it as effectively as they could? Maybe, maybe not. Each school culture is different, and schools with a higher disruptive element/ more social issues would understandably need to use it more than a leafy school in a 'naice' area. In 'naice' schools it may well be that uniform violations are treated like this because their behaviour thresholds are lower, or sometimes in rural areas detentions are not possible because of transport, so isolation is used instead.
In my 17 years working in schools, I've never seen isolation used as some kind of prison where kids are kept for weeks with nothing to do. That's nonsense.