Might be too specific of an issue, but here we go. In my setup, I have this mod with Lignumis + wooden logistics.
This mod overrides Lignumis' burner long inserter with its own, which is all fine so far. But when I change the config option to disable free long handed upgrades, the burner long hander costs iron to craft instead of wood and gold, which doesn't exist on Lignumis.

As an additional bug I just noticed, still relevant to Lignumis' progression with this mod. It turns out that because this mod replaces Lignumis' burner long handed with its own, you can't craft Steam long handed inserters at all, since they need the ones from Lignumis. This happens regardless of whether costless long handed upgrade is checked or not.

Definitely not out of scope; while it is annoying to catch them all, I do need to provide usable functionality in as many cases as possible (with regards to mods like Lignumis, which add new inserter variants).

For the first case, I forgot that burner long copies ingredients from the long inserter not the burner inserter (it's the only exception, since almost all other inserters copy from their base form, excluding the new burner variants). Updated to force-copy the burner ingredients for the burner long specifically.

For the second case, I probably should have implemented some kind of automatic catch before I remove the original inserter, to replace existing recipes that use it, but hopefully Lignumis is the rare exception to the rule, so I just did a quick manual patch for it for the two recipes that needed it.

As a surprising third case, I realized that I don't actually make long steam versions for the Lignumis steam inserters, so the costless upgrade setting wasn't affecting it. I decided not to replace the pre-existing steam long recipes, because it would be very annoying to programmatically replace both recipes (gold pipe vs pipe), since the main logic was only made to handle one recipe per inserter. So another manual patch job; costless enabled just removes the ingredients for both recipes to one steam inserter (and I kept the alt recipe, even though it's identical, to match the rows above)

All fixes implemented in v5.1.27 (hopefully didn't miss anything or introduce any new bugs)