To fix this, I suggest that the defaults be adjusted so the conffile is really just for local overrides rather than distribution-shipped defaults. You could patch upstream to change the defaults to what you want so shipping a contentful conffile becomes unnecessary. Or you could add support to have distribution defaults ship somewhere read-only (eg. /usr/share) and have /etc/waagent.conf available for local overrides. For example, systemd does this with /lib/systemd/system and /etc/systemd/system. Or you could use a conf.d scheme, though I think that would only mitigate the problem rather than solve it.
To fix this, I suggest that the defaults be adjusted so the conffile is really just for local overrides rather than distribution- shipped defaults. You could patch upstream to change the defaults to what you want so shipping a contentful conffile becomes unnecessary. Or you could add support to have distribution defaults ship somewhere read-only (eg. /usr/share) and have /etc/waagent.conf available for local overrides. For example, systemd does this with /lib/systemd/system and /etc/systemd/ system. Or you could use a conf.d scheme, though I think that would only mitigate the problem rather than solve it.