Got the answer. Apparently whitespace is important. I changed:
container_commands:
01_setup_apache:
command: "cp .ebextensions/enable_mod_deflate.conf
/etc/httpd/conf.d/enable_mod_deflate.conf"
to:
container_commands:
01_setup_apache:
command: "cp .ebextensions/enable_mod_deflate.conf /etc/httpd/conf.d/enable_mod_deflate.conf"
and now it works.