Instead of modifying the existing chemical plants and refineries, what if it was a separate item? You could make the vanilla chem plant or the modded one, which would be it's own item with identical recipe. This would allow for building blueprints without breaking them, like space platforms which are a massive headache to redesign.

Thats not a terrible idea, my primary concern was getting the original mod updated to 2.1 while 2.1 is still experimental. I can look into that as an option if the original author doesn't update soon.