I agree with you mostly OP.
If children are allowed to get everything in a total mess then it ends up with no-one being able to play properly. Yes, at home if you want to play with your toy trains in the bath, that's fine, but at playgroup/nursery etc they should stay with the train track or there will be none there for anyone else to play with.
And yes, children should be able to lead their own play, but if they are not shown how to role play in the home corner, or use the play dough, or make the dolls house characters act out stories then their play is not going to be extended to the extent that it could be and they will continue to just rush about flitting from one thing to the next and leaving toys all over the place.
I did a day's supply work in a nursery once and stopped a child from moving the newly set out play dough from the play dough table. 'Oh no.' I was told. 'The children can use it anywhere to help their learning.' Well, within half an hour it was all trodden into the carpet, or dried out in little bits everywhere, so nobody could use it for any 'learning.'
In some cases, if a child is really making the most out of equipment and needs it in another area, then fair enough. But as soon as they have finished using it it should be put back properly so that it is ready for the next child. It's all very well saying 'let children play with things how they want' but when the next child arrives and the room is a mess with not one complete set of anything, how is that child supposed to know what to play? Chances are he or she will not be able to have a meaningful game as the equipment that might have been used is all mixed up.