With villains, Less is More. That is, the Villain shouldn't be the only thing the heroes have to face in the story. In fact, the main villain should have the least amount of presence in the entire story. But those few times he shows up, it is always dire and the heroes just barely escape. If your villain is doggedly perusing the heroes, have some brief moments of conflict, than let the villains plan for the next encounter. Show them tracking the heroes, or looking for hired guns to keep an eye out for them. What resources does the villain have at his disposal to do this?
Consider the first two Terminator Films, where the encounters between the Heroes and the Killer Robot are brief, but the villain's remaining screen time is pronounced by their actions building up to those encounters. In the first Terminator Film, Sarah, Kyle, and the Terminator (T-800A) don't meet each other for about a third of the film and the audience (and Sarah) are largely clueless to what the hell is going on, other then the premise. That said, we get clear character moments for all of them (Sarah being perfectly ordinary and only being mildly concerned with a news report that someone is killing people with her exact name). At the same time, we see both Kyle and T-800A go about arrival, gathering resources, and finding Sarah, and it's clear that Kyle is pragmatic, but he takes great pains not to hurt anyone and stay under the radar... meanwhile, T-800A will resort to brazen and unabashed violence if the "subtle" way doesn't work. In the entire run of the film, there are exactly two encounters where Sarah and Kyle and the T-800A are able to visually see one another during the sequence (The Night Club fight and the Climax). While the second act encounter at the police station they are close and both are aware the other is there, they never find each other. In fact, it's the build up to the escape that holds the audience's suspense as Sarah and Kyle are both confined in rooms that will keep them in, but will not keep the Terminator out... and the only fighting chance they have is to keep moving.
In the sequel, T2, the heroes (John, Sarah, T-800B (Bob)) face off against the shape shifting T-1000 Terminator (Liquid). The number of encounters where both the heroes and the villain are in line of sight of any party numbers rises in this film... to 3 encounters (The Mall fight, the Asylum Fight, and the Climax). In this case, there is a pattern repeat to the fight, with a public place, an imprisoning controlled environment, and an industrial sight after hours. It's also notable that while the resource gathering is less focused on to the build up to the first fight, the intended shooting was building up for a surprise... if you watch the film, it's never stated which side Bob and Liquid are on. The intent was to make audiences assume that Bob is the killer robot and Liquid is just a different type of hero than Kyle (much more violent prone and behaving in a much colder way). It's only when the first shots from Bob are fired are the audiences alerted to the truth (You can thank poor marketing for spoiling this twist, as they sold the film on Arnold is Back.. and a hero.). But the T-1000 is genuinly considered the more menacing character in this light because, while he's unsettling to the audience, he's actually better at interacting with humans than T-880A and Bob, at first.
Both also resort to watching family after losing the trail of their prey. In the first film, T-800A intercepts a phone call from Sarah to her mother to resume the fight... but he doesn't kill the mother (I recall) as it's not necessary to the job. But in T2, Liquid is much more brutal, and kills John's foster parents and replacing his foster mother. Upon realizing that his feint was scene through, both Bob and Liquid conclude that Sarah's life is in danger as she is the next likely relative to John that he can use to pick up the trail. After these two fights, the film pulls back Liquid and we focus on the heroes regrouping and trying to figure out their next move. Liquid spends considerably less time on screen during this point than T-800A, because he really does not have much more he needs to do... he already has access to communication networks that will likely report the heroes the moment they turn up. In that time, a number of conflicts between the heroes actually let the audience breath and take in the stakes. When it's time for the action to resume, both parties are following logical steps based on clues they find and resources available to them.
There was actually a period during the Pokemon anime's long run where Team Rocket were actually given a treatment to make them more of a threat. During the Black And White generations, the anime story took some turns to make Jessie and James more of a threat and gave them an important role in Team Rocket's larger efforts for the seasons during this generation which received mixed receptions (Japanese audiences actually love Team Rocket's hapless antics. Western Audiences liked that Team Rocket were given some actual menace and competency to break their schtick. Subsequent Generations would see Jessie and James appear less frequently, however, reverted their appearances back to their usual silly antics, which compromised the two divisions and would keep this formula until their announced retirement from the series as it enter the 9th Gen era). So it shows that it would work with even your bad examples.
Additionally, as your genre is survival horror, keep in mind that often the staple of the genre is that the true antagonist is the environmental hazards. Even if you have a villain, heroes of survival fiction will often be antagonized by an indifferent nature that they are forced to adapt to in order to survive. A villain is always a personified figure of opposed morality to the intended message of the work of fiction. An antagonist need not be human or directly opposed to the hero. It merely has to be obstructive to the hero's own goals. Thus, if you want important moments of antagonism for your hero, but don't want the villain, your genre should easily provide some good antagonists that you do not need to motivate. A predatory animal facing off against the hero doesn't care why the hero needs to get to where it is going. It merely cares that the hero is made of meat and it is hungry.
Additionally if traveling in a group, the group's interpersonal conflicts can be antagonistic. If you watched Avatar: The Last Airbender, the first episode after Toph joined the team sees the heroes on edge and ready to kill each other because they are being chased by an unknown group that they want to avoid for the sake of possible danger and cannot get any rest (Like the terminators which will not stop in their quest to kill their targets. The unstoppable hunter is a persistent trope in fiction because this type of hunting is actually something humans understand well. Humans are probably the king of animals in long distance endurance, and back when we were hunter gathers, we would often track and follow animals until the gave up in exhaustion. It's essentially being hunted by someone or something that may be better at what we do best than we are.).
So your villain can still get his scenes in and be menacing, by letting him repeatedly regain the trail. Some of the other adventures in the heroes trip will result in that trail resuming. They might not meet, but the threat is that he's still chasing you.
