I don't exactly know about whether I'd say it's threatening or not. At least not to me since I accepted that I die alone before I even got out of high school.
It's just I know what I like to read. If I want to look at lesbian content like that then there's plenty of websites, but when I click on a manga or fanfiction that says harem in it I expect a normal harem. Not a single pairing, open-ended ending where there's no pairing, or (which is much more common in fan fiction) a orgy pairing where the girls bang each other for no damn reason despite saying how they love only the mc. It just really ruins the plot for me. It basically feels like ntr or cukoldry or whatever the hell it's called.
By threatening i mean they don't regard lesbian relationship to the same level as heterosexual. A lot of them don't understand that a lesbian can take away your partner just as easy as a guy (if not easier).
For example i regard a lesbian who actively uses her girl "privilege" to grope, watch or seduce in settings that would be regarded as sexual offense if made by men AS devious and trashy but Japanese populace doesn't regard it as something offensive. There are multiple scenes when a guy for accidentally seeing a girl naked or groping her get's physically and verbally abused WHILE at the same time a lesbian or a bi woman is given a free pass on that. In my opinion these women should be used as the same comedy relief as men otherwise it reeks of double standard.
As for harems in Japanese media......It's exactly what you dislike. In majority of harem-type mangas i see: Eventual single-pairing, open-ended ending where "we choose" and of course orgy where girls casually engage in sex between each other or at least flirt a lot. If not the whole harem then parts of the harem act lesbian but usually 1 one of them 100% does it.
I don't see normal harems in Japanese mangas, maybe 1 out 8 at best.