Also you don't strictly need to run a MU Domain Mapping plugin. You just need the domain to respond so Lets Encrypt can verify you control the site. Let's Encrypt puts a file in the root directory and verifies that it can access that file over the Internet.
Here are instructions for mapping a domain name without a plugin: https://wordpress.org/support/topic/howto-domain-mapping-without-a-plugin-instructions/ and https://halfelf.org/2014/mapping-domains-without-plugin/ The only thing you need to watch out for is setting the COOKIE DOMAIN to the proper value otherwise WordPress won't let you login https://handbuilt.co/2016/07/07/fixing-cookie_domain-for-mapped-domains-on-multisite/