I think, that this is not only a valid (and unanswered) question but also a valuable "enhancement request". Not only for Graylog use case ...
from me: +1
Because rsyslog config via GUI is very rudimentary, an option to use a custom rsyslog.conf could be helpful.
Is there a recommendation to tune rsyslog via snippets in /etc/rsyslog.d/*.conf
Best regards
Oliver