I have no experience with containers so forgive me if I'm missing something.  
Why couldn't you just have a 'microinit.rpm' in a separate dnf repo, put 
'Obsoletes: systemd' into that package?  This way people who are building 
hundreds of containers that do not require systemd can use the repo containing 
microinit and it will take the place of systemd.  RPM macro's could be provided 
by the microinit rpm, so it would provide reasonable replacements for 
%systemd_requires, %systemd_post, etc.  I think this could solve your concern 
with minimum (no) impact to bare metal installs.
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