I was running ToT when I saw that I saw that for each item that could drop, there was a duplicate but just thunderforged. I don't know if this was intentional or not, but it pretty much made my percentage drop by about half. Is there a way to turn it off, because I don't really like the idea of relying on rng upon already existing rng just to collect the appearance again for the same item.

No, Titanforging is not filterable nor will be.

If you are running Unique mode when you collect the base appearance or the Titanforge it counts for both. If you are doing Completionist then you'll need both items. This is just unfortunately how Blizzard coded the items.

Also, the Titanforged items have always been there and counted against your numbers. It's just that they were linked to the original weapon causing people to think it was a turn-in upgrade.

This is working as intended.