I think it's the same reason Windows feels easier than Linux to manage software in, or why Docker has the extremely fast and wide adoption it enjoys, or why so many of us
hate working with modern web stack.
Windows software is often enough "portable executables" that can run off the folder they were unzipped into, and historically, even installed apps could often enough be copy-pasted from their installation folder into another machine and Just Work (it was helpful, in particular, that all the DLL files lived next to the executable instead of being installed system-wide).
Docker, obviously, because it eliminates all the bullshit of installing software - again, especially painful on Linux systems - and gives you a single file that drives it all. The platform itself may be system-wide, but the thing you care about: individual software - is contained (literally) so it doesn't spill out. Easy to reason about.
Modern web stack is a mess of tooling, some of which system-wide (so people will reach for Docker to contain it all!), with huge version churn and lots of moving pieces. Source code of your app doesn't feel like a major component of it; it's useless and unparseable without chains of finicky tooling. That's in contrast to "vanilla JS", old-school experience, where source files were the only thing that mattered. No transpilation, no build chains. You could fire a site up straight from your hard drive, or FTP/SCP it to a file host, and It Would Just Work.
Same with SQLite. To this day I don't like RDBMSes, because they're a system-level platform designed for admins, while all I care about is the RDB part. My database. SQLite maps conceptually to how I think about it - one database, one file (+/- WAL). One well-defined place my data lives, that I can move around and between machines using regular file operation tools.
Etc.
Files over apps, always.
EDIT:
This also makes me very eager to try doing something with RedBean[0] - a webserver in a single Actually Portable Executable[1] that's also a ZIP file into which you put all the data you want it to serve. A turn-key website in a single file!
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[0] - https://redbean.dev/
[1] - https://justine.lol/ape.html