Well, it would in the sense that JkMount would dictate to Apache where to find files. So, the Certbot --webroot-path would have to match where that is. It replaces DocumentRoot essentially.
I am pretty sure they could leave JkMount out of the port 80 block entirely and just specify DocumentRoot to match the --webroot-path. I don't have Tomcat to test with but I presume DocumentRoot would work fine by itself.
Another option if they really want JkMount is to use JkUnMount for the acme challenge folder. I don't know Tomcat very well so I suggest this only from their docs. And, it seems unnecessarily complicated compared to just using DocumentRoot.
Generally I think it is bad idea to use --apache plugin for Tomcat. The --apache plugin is not tested with any Tomcat extensions in the Apache config file so results unreliable.
They could even consider just using Apache as a standard reverse proxy to their Tomcat system and not use JkMount at all (anywhere).