You should be able to just throw them in from the top, although there’s apparently an issue with mincraft’s fantastic collisions that often catapults the items out of the crucible on servers. To combat this I wanted to add hopper compatibility but forgor 
As for why malachite dust blocks don’t work at all, it’s probably because NTM doesn’t directly use GT6’s material system and instead works off of a small list of OD prefixes (with some GT6 compat slapped on top), and there’s no prefix for dust blocks. If you have some prefixes that would be useful, let me know.