Editing to add a link to this Apple support article which is unsurprisingly detailed - https://support.apple.com/en-us/149555
Similar reason (though with the opposite effect) as how a cert can be fine for browsers but fail for curl when they don't send an intermediate: the "vanilla"/library/command-line stuff is just checking for a path to a trusted cert and not doing the CRL or AIA stuff a browser does.
CLI-based activity references etc/ssl/cert.pem. While they say this will be updated in the future (likely the next dot release), admins can also proactively remove the eMudhra entries.