An incomplete or incorrectly ordered certificate chain can cause trust errors even when the leaf certificate itself is valid. The SSLFOR Certificate Chain Builder accepts a server certificate plus one or more intermediate or root certificates, identifies issuer relationships, verifies certificate signatures where supported, and orders the chain.
When a self-signed root certificate is supplied, the tool identifies it and omits that root from the server fullchain download. Web servers normally send the leaf and required intermediate certificates while clients already maintain trusted root stores.
The generated fullchain.pem is intended to make chain deployment clearer, but always follow the exact certificate-file directives required by your web server, load balancer or control panel.