I tried removing and reinstalling e2fsprogs, and it made no difference.
# pkg check -s e2fsprogs
Checking e2fsprogs: 0%
e2fsprogs-1.45.6_5: checksum mismatch for /usr/local/sbin/e2fsck
e2fsprogs-1.45.6_5: checksum mismatch for /usr/local/sbin/fsck.ext2
e2fsprogs-1.45.6_5: checksum mismatch for /usr/local/sbin/fsck.ext3
e2fsprogs-1.45.6_5: checksum mismatch for /usr/local/sbin/fsck.ext4
e2fsprogs-1.45.6_5: checksum mismatch for /usr/local/sbin/fsck_ext2fs
$ uname -mrs
FreeBSD 12.2-RELEASE-p1 amd64
$ cat /usr/local/etc/pkg/repos/FreeBSD.conf
This is a known issue due to a pkg limitation.
We need to have the same executable accessible in $PREFIX/sbin where it belongs, and under /sbin. In order to avoid packaging the same file twice, I could use symlinks or hardlinks. Hardlinks would break when pkg unpacks the package on installation in case $PREFIX/sbin were not on the same file system as /sbin.
The current solution is that the post-install script (pkg-install) tries to convert them to hard links on systems where this is possible. This happens without pkg's knowing and causes the checksum differences.
I'd previously tried to just linking or copyoing the files without packaging them, which caused PRs complaining that "pkg which" would't report which package the files originated from...
So some artifact will remain until pkg learns some "hardlink or copy" option.