So, how can I create a 'ISRG Root X1' chain certificate and why the R3 is also expired according to safari? If it is expired, why it's keeping signing new certificates?
Check that your website configuration is using fullchain.pem not chain.pem otherwise the client operating system will try to resolve the R3 > ISRG Root X1 etc itself and in many case (macOS etc) that will fail.