The ca-certificates RPM version 2020.2.41-1 (which is deployed by SailfishOS 4.1.0, 4.2.0 and 4.3.0) definitely contains the ISRG Root X1 certificate, see ca-certificates/ca-certificates.changes at master · sailfishos/ca-certificates · GitHub
Even older versions of the ca-certificates RPM have deployed it for many years.
Thus adding it a second time is not the crucial point.
But by putting it into the /etc/pki hierarchy, you changed its priority, for details see centos update-ca-trust man page on unix.com
This might hint the real cause for your issues and some analysis may guide you to a comprehensible solution.
For additional information and details WRT this topic, see