Suggestion to use OptiFine CIT for some items
I've looked around the wiki and some items after crafting appear as vanilla items. Since you're already using a resource pack, why not use OptiFine's CIT to make models of these new items?
I believe all previous instances of items looking like vanilla items have been replaced, though the wiki images may not be up to date. In general I try to avoid using Optifine as it's not always available and/or people don't, won't, or can't use Optifine. I would maybe consider some Optifine enhancements if it didn't affect users without Optifine.
one thing that particularly struck to mind was crafting the machine crafting table - it appears as a damaged anvil before it gets crafted.
yes it is a limitation of minecraft and we can not do anything about it