I have WP 4.3.1 (yes, will be upgrading to 4.4 shortly) and WP-CLI 0.21.1 installed on an en_GB locale WordPress system. wp-includes/version.php therefore has a different checksum from, say, the en_US locale because of the additional line at the end of the file:

$wp_local_package = 'en_GB';

However, if I then run this command from the Web tree root:

wp core verify-checksums

then I get this output:

Warning: File doesn't verify against checksum: wp-includes/version.php
Error: WordPress install doesn't verify against checksums.

I've md5sum'ed wp-includes/version.php and compared it with the md5 checksum here:

http://api.wordpress.org/core/checksums/1.0/?version=4.3.1&locale=en_GB

and it matches correctly, so wp-includes/version.php hasn't been modified.
If I then run the same command, but using the 0.20.1 wp binary, I get this:

Success: WordPress install verifies against checksums.

My suspicion is that WP_CLI 0.21.1 isn't checksumming non-en_US locales correctly.