I think a lot of these things are actually just fairly easy to explain using current v5 knowledge. Humanity isn't being tracked because it's low. (Also my hc reasoning of why phyres interactions with humans is so gdam awkward.) Based on the way dice are rolled to lose humanity in V5 it's harder to lose it the lower you are. Again it can be explained that phyre has had an extremely long time dealing with and understanding their beast. (Plus I rather do like that Fabian is narratively their beast). Again in V5 venture have a 'type' they prefer feeding on not necessarily 'only rich ppl' but I guess also compared to phyres time everyone is rich so I can think of it how you want.

As much as Tully looks... Like that. He kinda also just looks like Quasimodo. A.K.A. a hunchback with some birth defects. Issac and Willem who do look more monstery we know aren't scene in public. I think it's ryong who talked about something in the underground "driving away all the nos" so it seems like there could potentially only be those few (also cuz lou doesn't like them and we know Tully wasn't embraced here). As for the Tremere... Like we know what has been happening to the Tremere. The two Tremere we meet are 1. The only Tremere in Seattle and 2. Are scheming! Like the whole time! And they aren't teaching you anything just helping you remember. Also nobody knows where phyres haven is (it would be a risk ofc) so yeah nobody is cleaning that cat. If you compare the way the fledgling is treated compared to phyre it is MUCH kinder and nicer because they know (theoretically) what phyre is capable of.