I'm unable to confirm your problem, however I can confirm that
MSYS2 surely has many troubles in correctly supporting the
this is what I can see on my own mingw32.exe / mingw64.exe shells:
a. spatialite_cli.exe is unable to show any output at all on
the console's screen
b. and the same is for sqlite3.exe from the canonical "pacman"
distribution in -/mingw64/bin
both the stdout and stderr files work nicely when redirected
as e.g. in
spatialite >out1 2> out2
they correctly work on the MS cmd.exe command shell, and the
same code works nicely on Linux.
my personal conclusion is that MSYS2 has some obscure
idiosynchrasy forbidding to correctly hanlde stdout
and stderr in the same way supported by native cmd.exe