Since the merge of all bfa together and the plugin has been not that useful for me, all rares are showing to me and I dont care for them.

Previously I had only toys/pets/mounts tick option and these are the only things I want to track, i.e. I want the blue skull to show only for these, but now its showing for everything, I dont care for weapons, or transmog, how do I disable these?

There will be some options in one of the upcoming releases to filter different types of rewards from the tooltips.

The upcoming release has an option to turn off transmog rewards.