If low-risk HPV is so common & acts similar to flu or chickenpox; symptoms treatable, system weakens virus, why is it so stigmatized as threatening?

Because of sex. Two main reasons. First, HPV is sexually transmitted, and throughout history most societies have had negative views about sex and see STDs as embarrassing and frightening. Second, warts, the main problem from low risk HPV, have a "yuck" factor. Even common hand warts often are considered unclean (e.g folklore about catching them from toads), and many people consider genital warts especially gross.