Or users could simply get confused about what to do with those files and contact support a million times just to ask why these files exist, whether they need to be copied as well, why they are getting large, etc.
These issues can be worked around, but I wonder how many apps that use SQLite actually bother doing that. Clearly not all of them [2].
Avoiding file corruption is non-trivial regardless of file format, but giving users additional ways to corrupt their data is never a good thing.
So I think for small, user visible application files that don't need any database functionality, the onus is still on engineers to justify their choice of SQLite.
[1] https://www.sqlite.org/howtocorrupt.html
[2] https://forum.audacityteam.org/t/aup3-wal-file-remains-and-l...