With MysticalAgriculture 1.6.4, Forge 2478, Refined Storage 1.5.18, and Minecraft 1.12.1; there is no recipe to craft silicon from silicon essence. I can craft quartz enriched iron from it's essence.

This is because refined storage registers oredictionary entries during the same event as I register recipes, so load order becomes an issue.

Is this something I can work around? Force the load order? Or do you know how to fix it?

You can add your own recipes with crafttweaker
The refined storage devs could register items in the oredictionary when they register items

The refined storage author replied: "When you register recipes that are other mod dependant you probably need to be registering recipes in postInit."

It's worked up to this point, and this is the only issue with it, so I guess we'll just have to live with it.

I'll probably just add another recipe for it whenever I start working on the next update.

I've added craft tweaker and I'm using that, thanks for your attention, and the mod, I love it.

Looking at CraftTweaker, will log a request with Refined Storage, could you add a config option to force the recipe creation? I'm guessing not because you don't know what the item to be created is :(
Thanks for your prompt attention.