~/certs and ~/.acme.sh for the acme user and provide a sample account.conf
You cannot put sample files in there. You have to move them somewhere else, like EXAMPLESDIR.
So all the files in there are always used. If you put a .sample file, it will be used.
Also, the file should probably be named acme.sh, and not the very long name you have now.
/usr/bin/install -d -o acme -g acme -m 750 ~/acme/.acme.sh
/usr/bin/install -d -o acme -g acme -m 750 ~/acme/certs
I would use %%EXAMPLESDIR%% directly here, no real need to create a variable.