I use logistics to change recipe's in the Synthesizer - but I can't do that if the ports are not consistent.
https://imgur.com/a/EUJ1Cqy

Any chance you would change contemplative replication to have water come out opposite the matter replication gel. This would be consistent with Widget Replication and basic matter replication. I haven't gotten further than this yet, so I can't comment on other recipes.

I played first time complaining that the buildings should take logistics, they do - but it has to be turned on, requiring a restart. That should be the default option.
Thank you - great challenge !