According to the syncevolution doc, the location of the certificates
used to authenticate the server is configurable through 'SSLServerCertificates' configuration property.
This property is set by the 'config.ini' files in the home directory:
phablet@ubuntu-phablet:~$ grep -rIn SSLServerCertificates .config/syncevolution/
.config/syncevolution/default/peers/google-calendar-2/config.ini:# SSLServerCertificates = /etc/ssl/certs/ca-certificates.crt:/etc/pki/tls/certs/ca-bundle.crt:/usr/share/ssl/certs/ca-bundle.crt
.config/syncevolution/default/peers/google-contacts-2/config.ini:# SSLServerCertificates = /etc/ssl/certs/ca-certificates.crt:/etc/pki/tls/certs/ca-bundle.crt:/usr/share/ssl/certs/ca-bundle.crt
.config/syncevolution/google-calendar-2/peers/target-config/config.ini:# SSLServerCertificates = /etc/ssl/certs/ca-certificates.crt:/etc/pki/tls/certs/ca-bundle.crt:/usr/share/ssl/certs/ca-bundle.crt
.config/syncevolution/google-contacts-2/peers/target-config/config.ini:# SSLServerCertificates = /etc/ssl/certs/ca-certificates.crt:/etc/pki/tls/certs/ca-bundle.crt:/usr/share/ssl/certs/ca-bundle.crt
So, you can add or edit these configs to additionally point to some .crt in the home dir (which is writable).