Now that the R3 intermediate is in place is the preferred-chain option live to allow clients to request the old DST chain?
I tried requesting a cert with the 'DST Root CA X3' chain using the certbot 1.10.1 client and it seems like the cert is still being issued by the new R3 intermediate.
I double-checked the debug log and the correct '--preferred-chain' argument is being parsed but when I look at the cert issued it still shows:
$ openssl x509 -in cert2.pem -text -noout | grep -i iss
Issuer: C=US, O=Let's Encrypt, CN=R3
CA Issuers - URI:http://r3.i.lencr.org/
$ more /var/log/letsencrypt/letsencrypt.log
2020-12-21 14:13:53,705:DEBUG:certbot._internal.main:Arguments: ['--manual', '--preferred-challenges', 'dns', '--force-renewal', '--preferred-chain', 'DST Root CA X3', '--manual-auth-hook'
Your certificate will always be issued by R3. Certbot does not have any choice in that respect.
Where --preferred-chain makes a difference is choosing between a version of R3 which is highly compatible (R3's issuer is "DST Root CA X3") or the modern one with slightly less compatibility (R3's issuer is "ISRG Root X1").
The ability to make that choice has been live for quite a while now.
In this case the issue is that some services (Subscription Manager / Foreman RedHat Satellite specifically) verify the entire chain against one installed/stored from an RPM and changing the intermediate will break the verification.
Happy Holidays
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So they verify not only the root but also the intermediates as a whole? Change out the intermediate and the chain breaks?
Well, that's an incorrect design choice. Intermediate certificates can change at any notice. For example, if suddenly there would be an incident with the R3 intermediate, Let's Encrypt can fallback to their backup intermediate R4. This could literally happen at any time, without any warning. Pinning intermediate should never be done.
Also, because I can't actually believe that Redhat would do such a thing: do you have proof of your statement?