None of the things you're saying sound like they're from any of my mods.
I have no idea what a Crystallizer is, or any of the other things you've mentioned. Slag processing sounds like it's an Angels thing, this isn't Angels mods.
The only "Interference" Bob's mods do with Technologies is part of the Library mod, and it's a "Clean up" run in data-final-fixes, who's sole purpose is to remove redundant prerequisites, and fix issues such as science packs being present on the list multiple times. The code would detect those duplicates and change it to cost 2 of the science pack, rather than 2 instances of the same, as the game crashes if you list it twice. It does similar things with Recipes too, removing items that don't exist, and consolidating duplicates where possible. (Since it's in data-final-fixes, nobody should be creating or editing technologies in this step, but some people do, which is why the cleanup script doesn't catch and fix all technology and recipe based errors)
And it does all of this in the database construction phase, while the game is loading after you double click on that Factorio icon on your desktop (Or however you launch the game). It doesn't do anything while you're loading a savegame, or after it's loaded, so it can't change what you have and haven't unlocked.
