Add an option to hide/disable the normal-sized version if you wish, for your micro mod add the same, either hide it from the player build menu or disable it completely if you toggle the option on

Not sure how I missed this suggestion from 8 months ago, but I think a setting like this might introduce a ton more issues. This mainly applies to other mods, but it happens in vanilla as well, if the base machine is used in a recipe (like electric furnace in purple science), and I hide the base machine from the crafting menu, then you won't be able to craft that recipe.

I suppose I could go through every recipe in the game, check if one of the base machines is being used, and replace it if necessary.. or alternatively, just hide the recipe from the player crafting menu, while keeping it in the assembler crafting menu (so you could still automate it). There would be incompatibilities if any mod loaded after this one, and overwrote the recipes to use the base machine again.