lets encrypt certificate for a 3rd party service on same server

I have inherited a server that have WHm/Cpanl installed but also has other independent services / servers side-by-side. I know it is not an ideal situation - but it is what it is. My question is as follows: The domain mydomain.TLD is registered and functioning properly on whm/Cpanel. it also has other subdomains working and with Auto-SSL configured . I want to use a specific single sub.mydomain.TLD to point to another service ( GOGS ) on the same machine that works with an independent Golang service. ( when I write "independent" i mean that it is installed outside of the capanl environment and has it's own services / server ). The doubt I have is how to generate / use the let's encrypt certificates from Cpanl/WHM in order to use HTTPS on the external service. I am afraid that if I will install the auto certbot "independantly" ( again ) it could somehow conflict with the other Cpanel AUTO-SSL on the main mydomain.TLD or any of it's subdomains . On the other hand I did not find any certbot on the system ( probably / maybe cpanel handled it differently ). Is there a way to generate a let's encrypt certificate from inside WHM/CPANEL and just copy the KEY and PEM files to the other "independent" location without causing chaos? Or should I just install the normal certbot alongside WHM ?