Huh, that's... weird. I don't exactly understand what Pacifist is doing to the recipe, or why it only messes up the tier 4 machine, but yeah, it seems to apply after everything else, during data-final-fixes. I only do recipe changes during data-updates, dependent on the modlist.
The vanilla recipe is supposed to use 2 electric furnaces, a reverse factory 3, and 2 efficiency modules, in addition to the 10 steel. It's possible that Pacifist mod is changing the structure of the recipe so that my existing functions can't properly add the new ingredients? Hmm.. no, as far as I can tell, my code is adding all of the ingredients correctly during data-updates, but something happens during data-final-fixes that removes all but the steel. I don't get it.
Tempted to just label this one as an incompatibility; it seems to be an issue with the Pacifist mod in some way, nothing I can do to fix it.