The top root certificate for any Certificate Authority is always self-signed (check out the Verisign cert at the bottom of this post) ... that's why you explicitly trust root certificates.
Fabric CA allows you to either specify an existing root key pair or if the specified files do not exist it generates them for you. (if the cert file exists but a matching private key cannot be found you'll get an error and fabric-ca-server will not start).
When fabric-ca-server generates its own self-signed keypair, it actually generates the private key in the msp/keystore folder but it will store the self-signed X509 cert in the file specified via FABRIC_CA_SERVER_CA_CERTFILE if specified else it will use the location in fabric-ca-server-config.yaml. Note that if you use the FABRIC_CA_SERVER_CA_CERTFILE override, the value is not updated in the config file (perhaps this is causing some confusion).
Verisign Primary
Garis-MBP:tmp gsingh$ openssl x509 -noout -text -in verisign.pem
Certificate:
Data:
Version: 3 (0x2)
Serial Number:
18:da:d1:9e:26:7d:e8:bb:4a:21:58:cd:cc:6b:3b:4a
Signature Algorithm: sha1WithRSAEncryption
Issuer: C=US, O=VeriSign, Inc., OU=VeriSign Trust Network, OU=(c) 2006 VeriSign, Inc. - For authorized use only, CN=VeriSign Class 3 Public Primary Certification Authority - G5
Validity
Not Before: Nov 8 00:00:00 2006 GMT
Not After : Jul 16 23:59:59 2036 GMT
Subject: C=US, O=VeriSign, Inc., OU=VeriSign Trust Network, OU=(c) 2006 VeriSign, Inc. - For authorized use only, CN=VeriSign Class 3 Public Primary Certification Authority - G5
Subject Public Key Info:
Public Key Algorithm: rsaEncryption
Public-Key: (2048 bit)
Modulus:
00:af:24:08:08:29:7a:35:9e:60:0c:aa:e7:4b:3b:
4e:dc:7c:bc:3c:45:1c:bb:2b:e0:fe:29:02:f9:57:
08:a3:64:85:15:27:f5:f1:ad:c8:31:89:5d:22:e8:
2a:aa:a6:42:b3:8f:f8:b9:55:b7:b1:b7:4b:b3:fe:
8f:7e:07:57:ec:ef:43:db:66:62:15:61:cf:60:0d:
a4:d8:de:f8:e0:c3:62:08:3d:54:13:eb:49:ca:59:
54:85:26:e5:2b:8f:1b:9f:eb:f5:a1:91:c2:33:49:
d8:43:63:6a:52:4b:d2:8f:e8:70:51:4d:d1:89:69:
7b:c7:70:f6:b3:dc:12:74:db:7b:5d:4b:56:d3:96:
bf:15:77:a1:b0:f4:a2:25:f2:af:1c:92:67:18:e5:
f4:06:04:ef:90:b9:e4:00:e4:dd:3a:b5:19:ff:02:
ba:f4:3c:ee:e0:8b:eb:37:8b:ec:f4:d7:ac:f2:f6:
f0:3d:af:dd:75:91:33:19:1d:1c:40:cb:74:24:19:
21:93:d9:14:fe:ac:2a:52:c7:8f:d5:04:49:e4:8d:
63:47:88:3c:69:83:cb:fe:47:bd:2b:7e:4f:c5:95:
ae:0e:9d:d4:d1:43:c0:67:73:e3:14:08:7e:e5:3f:
9f:73:b8:33:0a:cf:5d:3f:34:87:96:8a:ee:53:e8:
25:15
Exponent: 65537 (0x10001)
X509v3 extensions:
X509v3 Basic Constraints: critical
CA:TRUE
X509v3 Key Usage: critical
Certificate Sign, CRL Sign
1.3.6.1.5.5.7.1.12:
0_.].[0Y0W0U..image/gif0!0.0...+..............k...j.H.,{..0%.#http://logo.verisign.com/vslogo.gif
X509v3 Subject Key Identifier:
7F:D3:65:A7:C2:DD:EC:BB:F0:30:09:F3:43:39:FA:02:AF:33:31:33
Signature Algorithm: sha1WithRSAEncryption
93:24:4a:30:5f:62:cf:d8:1a:98:2f:3d:ea:dc:99:2d:bd:77:
f6:a5:79:22:38:ec:c4:a7:a0:78:12:ad:62:0e:45:70:64:c5:
e7:97:66:2d:98:09:7e:5f:af:d6:cc:28:65:f2:01:aa:08:1a:
47:de:f9:f9:7c:92:5a:08:69:20:0d:d9:3e:6d:6e:3c:0d:6e:
d8:e6:06:91:40:18:b9:f8:c1:ed:df:db:41:aa:e0:96:20:c9:
cd:64:15:38:81:c9:94:ee:a2:84:29:0b:13:6f:8e:db:0c:dd:
25:02:db:a4:8b:19:44:d2:41:7a:05:69:4a:58:4f:60:ca:7e:
82:6a:0b:02:aa:25:17:39:b5:db:7f:e7:84:65:2a:95:8a:bd:
86:de:5e:81:16:83:2d:10:cc:de:fd:a8:82:2a:6d:28:1f:0d:
0b:c4:e5:e7:1a:26:19:e1:f4:11:6f:10:b5:95:fc:e7:42:05:
32:db:ce:9d:51:5e:28:b6:9e:85:d3:5b:ef:a5:7d:45:40:72:
8e:b7:0e:6b:0e:06:fb:33:35:48:71:b8:9d:27:8b:c4:65:5f:
0d:86:76:9c:44:7a:f6:95:5c:f6:5d:32:08:33:a4:54:b6:18:
3f:68:5c:f2:42:4a:85:38:54:83:5f:d1:e8:2c:f2:ac:11:d6:
a8:ed:63:6a