When using a skin swapper mod, the hidden duplicate handcrafting recipes don't seem to be given to the non-default engineer skins, which forces handcrafting each component step by step.
In my case I'm using the !skins (Skins Factored) mod, but it might affect all skin swappers.
One of the skins I tested with was engineer tf2, but it appeared to affect any skin swapped to by !skins.

Also related to handcrafting; with the Lignumis mod recipes usually prioritise copper-based recipes instead of gold-based ones after they're researched. With Scrappy Industry installed handcrafting seems to prefer gold-based recipes, which is annoying for anything that uses its basic circuit boards (e.g. splitters) once you've left Lignumis. Though I'm not sure if this should be fixed by SI or Lignumis itself.

Compatibility with multiple skins has been added with a PR from S6X in 0.7.3!

Unfortunately unsure what to do about situations where multiple recipes exist. I may take a look at this later to see if there's a setting I can change on the hand-crafting recipes to fix this, but unsure I'll be able to promise anything.

0.7.3 seems to throw an error on launch:

Failed to load mods: __scrap-industry__/prototypes/recipe-final-fixes.lua:269: bad argument #1 of 3 to 'insert' (table expected, got nil)
stack traceback:
    [C]: in function 'insert'
    __scrap-industry__/prototypes/recipe-final-fixes.lua:269: in main chunk
    [C]: in function 'require'
    __scrap-industry__/data-final-fixes.lua:1: in main chunk

Huh, I'm unable to reproduce this with the skin mods I downloaded to test, but I've added in some fail-safe code so it won't crash at least. Characters that don't have crafting_categories defined will be left untouched, so if certain skins have difficulty with hand-crafting intermediates, let me know but I won't be handling compatibility with specific skins unless it's all skin mods, but I confirmed it works for e.g. Mechanicus at least.

Seems to launch fine now. None of the skins I have installed seem to have any problems (other than the duplicate recipe issue) with handcrafting now, might've been a mod using a dummy character for something, perhaps?

Thanks for the fix!