how can one ensure, when writing a psychological horror, that any supernatural/paranormal or just very unlikely element is not taken face-value?
Keep it ambiguous
Roald Dahl used to say that “The best ghost stories don’t have ghosts in them.” That means it's often better to preserve the ambiguity, than to allow the story to declare that something is definitively supernatural. Psychological horror takes advantage of the slow build of horror stories, and the ambiguity during that slow build to lay groundwork for a parallel psychological explanation that is unveiled either as a plot twist, or escalates along with evidence of paranormal as a competing theory.
Everything that is supernatural or paranormal is, by definition, defying the natural order – it's not possible according to the rules of the story universe. The natural order must be established before it can be threatened, or unravelled. Even as the paranormal incidents impose themselves onto the status quo, characters reject a supernatural explanation longer than the reader does. Putting the reader and MC at odds is unsettling and creates tension – we know something the MC doesn't, or isn't ready to face, and we see it as putting them in danger.
Magic breaks paranormal
If your story world includes magic, there is no such thing as paranormal so you can't score horror points for claiming so-and-so's magic is "natural" but la-ti-dah's magic is "un-natural". The reader has already bought into the idea that there is magic, so the natural order is not a given. Instead it is a setup for Dark Fantasy or Urban Fantasy where fantastical and powerful entities are things that exist. "Dark" magic might be tied to transgressive or morally evil side-effects, but it has no scariness just for existing in a world of magic.
Horror in general works better on the mundane, the domestic, and the ordinary. It is an attack on the status quo so there has to be a contrast. Paranormal needs a firm normal to contrast against or it becomes difficult to perceive any horror.
structure for psychological horror
The psychological horror story typically starts in the real world, and by stages convinces the reader that "paranormal is real", but then as the final twist turns the reader back to the real world when they ultimately reject an unreliable narrator, or discover the situation has been manufactured through gaslighting.
1. the plot twist
"The Yellow Wallpaper" by Charlotte Perkins Gilman is probably the grandmother of psychological horror stories where the psychological aspect works as a twist to an already disturbing premise.
the reader feels sympathy for the narrator believing her to be unfairly institutionalized, then alarmed by the disturbing descriptions of a crouching woman who haunts her, but ultimately rejects her as an unreliable narrator who is suffering from mental illness.
2. a competing theory
The Haunting of Hill House by Shirley Jackson uses psychology as a competing theory against the supernatural:
all of the researchers experience paranormal events, even together, and the house is given an explicit psychological profile along with its tyrant ghost. The house already has a reputation for being haunted, it's why they are there. The reader has more than enough evidence to be convinced of the paranormal, but the competing psychological explanation – that Eleanor is unreliable and staging events for attention – also grows, leaving an ending that feels ambiguous even though it shouldn't.
3. it's a metaphor
The Babadook and Annihilation personify psychology using monsters as a metaphor. The psychological explanation exists as subtext. Characters are proxies for psychological concepts, and the story works at two levels: objectively "factual" events which play as horror, and highly-symbolic cues which progress through the theme. Horror's suspension of natural order allows the narrative to emphasize the message within the subtext, without abandoning the horror plot.
Alfred Hitchcock's Psycho and The Birds are structured to tell a psychological analogy as the story itself. The analogy imposes onto the narrative, breaking the rules of character and pacing to create a meta experience for the viewer that is unsettling and unexpected.
Link spoilers: Understanding Psycho, Why Do the Birds Attack
Monster metaphors are not new: Moby Dick for obsession, Godzilla for nuclear weapons. A relative in the attic was a gothic metaphor for inherited insanity (or syphilis), and Strange Case of Dr Jekyll and Mr Hyde by Robert Louis Stevenson is a metaphor (a parable?) of cocaine addiction.
Perhaps society's perceptions of mental illness is evolving. It's no longer enough to simply go gibberingly insane from a Lovecraftian meltdown because "thing exists". Psychology today has its own mythos and recognizable states – some real, some cliché.
Unfortunately there are still bad-psychology throwbacks like Identity (2003) where
a serial killer and his victims are all multiple-personalities in one person's mind, fighting for dominance. Certain events are unexplainable except through horror tropes, like the killer having paranormal abilities, a la Jason Vorhees from Friday the 13th franchise, and their futile attempts to leave the motel seem fatalistic. The film turns first to horror/paranormal tropes, before revealing a pseudo-psychological explanation.