It’s difficult for me to say how common those phrases are. I know what they mean, but I myself have never used any of them. I find “per se” rather formal and would instead say “in itself”.
You could use “per se” in examples like these:
“The drug is not harmful per se, but is dangerous when taken with alcohol.”
“Research shows that it is not divorce per se that harms children, but the continuing conflict between parents.”