I just ran a few tests with a Debian Stretch test VM, default settings.
# cat /etc/os-release
PRETTY_NAME = "Debian GNU/Linux 9 (stretch)"
# wget https://letsencrypt.org/certs/staging/letsencrypt-stg-root-x1.pem
# wget https://letsencrypt.org/certs/staging/letsencrypt-stg-root-dst.pem
# cat letsencrypt-stg-root-dst.pem letsencrypt-stg-root-x1.pem > certs-combined.pem
# openssl version
OpenSSL 1.1.0l 10 Sep 2019
Simulating that only ISRG Root X1 is in the trust store:
# openssl s_client -connect expired-root-ca-test.germancoding.com:443 -servername expired-root-ca-test.germancoding.com -verify 1 -verifyCAfile letsencrypt-stg-root-x1.pem
-> Verification: OK
Simulating that only DST Root CA X3 is in the trust store:
# openssl s_client -connect expired-root-ca-test.germancoding.com:443 -servername expired-root-ca-test.germancoding.com -verify 1 -verifyCAfile letsencrypt-stg-root-dst.pem
-> Verification error: certificate has expired
Simulating that both DST Root CA X3 and ISRG Root X1 are in the trust store:
# openssl s_client -connect expired-root-ca-test.germancoding.com:443 -servername expired-root-ca-test.germancoding.com -verify 1 -verifyCAfile certs-combined.pem
-> Verification: OK