Hi @spygerm,
All Let's Encrypt certificates are generated by software; they're never generated manually and there is no way to override the automated processes.
I would suggest that you should ask Hostgator's support for help with this. Per a previous thread
using Let's Encrypt may not be a cost-effective choice for Hostgator customers because they were reported to charge a $10 fee to install a certificate. Since Let's Encrypt certificates expire every three months, this means at least $40 in fees per year, which is more than the cost of getting a year-old certificate from a paid DV CA and paying Hostgator to install it once per year.
Many hosting providers do not charge a fee for HTTPS support or for installing certificates, so you could also consider one of the providers on the list at