Alright, so this gave me quite a headache. I used the block editor to create new recipes for the factories, Personal Capsule Refinery, Micro Assembler, and the "Make Macro Factory Block." I then saved the output to a "BlockConfigImport.xml" file and put it into the "\StarMade\customBlockConfig" folder. On both single player and on our server for Light vs Dark, the recipes in the factories showed up with no problem. However, the capsule refinery, micro-assembler, and personal crafting recipes did not.
So, I tried instead to replace the "BlockConfig.xml" file in the "StarMade\StarMade\data\config\" folder. This worked to enable the rest of the recipes. However, this is not a good solution for our server because the "BlockConfig.xml" file will be wiped out every update and have to be replaced again.