If he's a boy kitty then no confinement is needed. Neutering the boys is no big deal and they are out and about in no time.

If he has been so long in the crate his urine will have been very concentrated and smell bad. Cat spray is basically urine and it will smell less if there are no more hormones produced -but not smell totally neutral. I suppose it is also possible that the hormones are still in the blood immediately after neutering.

Tell him he was a very good boy not to just pee in the crate. My boys would have done so