I spun up a new server and did a fresh install of IPA.  On that server if I run 
the command I get a better result

# openssl verify -verbose -show_chain -CAfile /etc/ipa/ca.crt 
/var/lib/ipa/ra-agent.pem 
/var/lib/ipa/ra-agent.pem: OK
Chain:
depth=0: O = AUTH.****.NET, CN = IPA RA (untrusted)
depth=1: O = AUTH.****.NET, CN = Certificate Authority

So I must be missing something with the RA cert.  It's definitely in LDAP.  
I've read that it should also be present in /etc/httpd/alias/ NSS DB, but that 
directory is empty on the fresh install so I cannot confirm.
The ASN.1 appears to be correct on the ra-agent.pem when I check

$ openssl asn1parse -inform pem -in ra-agent.pem
37:d=5 hl=2 l= 3 prim: OBJECT :organizationName
42:d=5 hl=2 l= 14 prim: UTF8STRING :IPA.****.NET
58:d=3 hl=2 l= 30 cons: SET
60:d=4 hl=2 l= 28 cons: SEQUENCE
62:d=5 hl=2 l= 3 prim: OBJECT :commonName
67:d=5 hl=2 l= 21 prim: UTF8STRING :Certificate Authority
90:d=2 hl=2 l= 30 cons: SEQUENCE
92:d=3 hl=2 l= 13 prim: UTCTIME :240322132444Z
107:d=3 hl=2 l= 13 prim: UTCTIME :260312132444Z
122:d=2 hl=2 l= 42 cons: SEQUENCE
124:d=3 hl=2 l= 23 cons: SET
126:d=4 hl=2 l= 21 cons: SEQUENCE
128:d=5 hl=2 l= 3 prim: OBJECT :organizationName
133:d=5 hl=2 l= 14 prim: UTF8STRING :IPA.****.NET
149:d=3 hl=2 l= 15 cons: SET
151:d=4 hl=2 l= 13 cons: SEQUENCE
153:d=5 hl=2 l= 3 prim: OBJECT :commonName
158:d=5 hl=2 l= 6 prim: PRINTABLESTRING :IPA RA


This was another cert that had an incorrect Principle attached and was 
regenerated.  I may have messed up something there, but I'm not sure what.
I do have a copy of the ra-agent.pem (and matching key) with the correct 
Principle from 2019.  I can put this in place on the broken server, but even 
with rolling the time back I'm not sure it will get renewed.
--
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