I've always used a catch cup to keep the urchin pretty much submerged. Some of them can be pretty picky about being exposed to air.
My tuxedo doesn't care, I've picked him up with my hand and moved him from tank to tank several times.
I also have a rock boring urchin who comes out at night mostly....(they mostly come out at night...mostly....
).
My long spine certainly never punctured any softies, they are very sensitive to feeling what is around them in my observation.