I think partially because the modders don't have to animate walk cycles and limbs moving, the train is mostly static. Also it's the contrast between horror and Thomas's squeaky clean branding.
He's also a double non-sequiter in most games he's modded into. Not only are there no trains, there are no trains with faces.
He stands out instantly as out of place in a way that some other in-jokes might not. Hank Hill might not look super weird in Left 4 Dead; presumably a number of middle-aged Southern men with an avid interest in propane were caught in the zombie apocalypse.
Because of this, it's funny even if you don't know who Thomas the Tank is. I think this is part of the reason for Shrek memes persisting as well (in addition to Shrek's extremely dedicated fanbase).
I think there's also the uncanny valley creepiness of Thomas's face, particularly within the context of an actual horror game. Hilarious to think that something so genuinely terrifying could come out of a children's show.
Terrifying for you but my two and a half year old has absolutely loved Thomas for almost half her life. She has Thomas toys, clothes, books, dvds, had a ride-on electric Thomas complete with circular track that took up most of the living room, and we took her on the life-size Thomas train in Pennsylvania twice. Thomas is absolutely her jam, followed by Lightning McQueen and then Elmo. Her nostalgia will obviously be different than our nostalgia, but it's nice to see the joy it brings her.
The RE2 mod footage makes me think about and feel like Silent Hill. Things make no sense in a nightmarish way because wetware tries to process them into something that almost individually makes sense yet violently conflicts with other elements that also almost make sense, but combine into an overarching distressing cognitive dissonance which causes unsettlement and terror.
I think this causes much less distress during youth because you've not been exposed to so many complex things with such regularity and over such a long period as you have later on, so you don't really unconsciously think "this is a face; no, wait, a train. wait, the bars on the wheels, they're kinda like where arms should be. are they arms? no this is a train. no ears, no hair, this is not really a head. Of course it's a train, but it's smiling. so it has a mouth, but no limbs, how does it eat? is someone and feeding it with charcoal by entering it from the back where the butt should be? WHERE ARE THE VISCERAS?"
Just regarding the face, it's kind of like the comment says in this video[0], somehow at 3:19 they're ok because they're abstract enough, at 4:02 they're fully entering the unsettling uncanny valley, but at 5:55 they look fine. And here you can fully extrapolate a matching body in your mind, but not with that hellish train, where the extrapolation projects such a body onto the train thing (and the other way around).
There's an undercurrent of existential horror entirely intrinsic to Thomas the Tank engine which already contrasts with the superficially happy and brightly-colored children's show. Putting Thomas in incongruous or unsettling situations throws this into sharp relief. Just what is Thomas?
I've been watching a lot of Thomas with my kid and yea it seems to somehow be a nightmare dystopia underneath even though nobody can explain why.
Stephen King's The Dark Tower spoiler below:
Stephen King's masterpiece "The Dark Tower" series has an intelligent AI in the third book called "Blain the Train". The dark tower series starts off as a kind of medieval Western in some barren dessert world and pretty soon there are doorways to parallel worlds and times like New York City. One parallel world was once populated by a society that is probably a few hundred years ahead of us technologically speaking, but they were warlike and killed themselves off. All that is left is Blaine the Monorail and Patricia the Train and they are super homicidally insane. I've been scared of Thomas ever since.
"Part of it, perhaps, is that Thomas and his world are innately horrendous, and there’s something horrendous about taking all that off the rails and into a digital space. The original books, penned in the 1940s by the Anglican reverend Wilbert Awdry, now read like an enthusiastic allegory for bigotry and exploitation. The New Yorker, among other publications, has a ghoulish piece of essayistic fiction on the drizzly dystopia that is Thomas’s Island of Sodor, where cheerful anthropomorphic machines are torn apart, worked to death or bricked up in tunnels at the whim of a well-heeled Fat Controller. For all its dark corners and clutching cadavers, Resident Evil 2’s setting can seem almost benign by comparison."
(Another show with cheery, brightly colored human-machine hybrids existing in a highly regulated totalitarian structure is Teletubbies, although it's more of a Brave New World to Thomas's 1984. You do see creepy Teletubby "cursed images" from time to time...)
The bricked up in tunnels example was pretty horrifying. Like I know they want to convey the value of hard work, but that is some Cask of Amontillado level crazy.
My toddler asks to watch that one most days and it is just horrible! Especially when the episode ends with Ringo saying "I think he deserves his punishment, don't you?"
This particular episode horrifies me; I feel like kids will grow up and as adults, look back on this and wonder how they didn't realize how dark it was, much like I do with some parts of things like The Brave Little Toaster.
My son has a Thomas the Tank Engine megablocks set, and he recoiled in terror when he first unearthed the Thomas-face block. Like, inconsolable crying @ 18 months. There is clearly a instinctual aversion to those out of place human features. Reminded me of the scene in Alien Resurrection with the failed clones.
He still has the blocks, but poor Thomas is no more.